Israel don't have the conventional munitions launched from aircraft to do deep damage to Iran's underground facilities, which is why Netanyahu was talking about commando raids and so forth. Israel fundamentally lack this capability. They could carry out a weeks long campaign repeatedly bombing tunnel entrances and attempts to rebuild them making operations difficult, but that's different from destroying the facility itself.

As for what could be done, even though it's unlikely:

On the conventional front, what Israel could do is take a page from South Korea's latest ballistic missile, and rig up one of their Jericho III ICBMs with a very large conventional bunker buster warhead and use it over the much shorter range towards Iran. The South Korean Hyunmoo-5 is a 300-3000km range, 36 ton two stage solid fueled ballistic missile (the same size and weight as a Minuteman III ICBM) with an 8-9 ton "bunker buster' warhead that can penetrate over 100 meters.

On the nuclear front, a very low yield "bunker buster" warhead delivered by a Golden Horizon air launched, maneuvering re entry vehicle capable ballistic missile, could be a tempting option for Israeli commanders. The planned, but eventually cancelled, W-86 nuclear Earth Penetrating Warhead (EPW) for the Pershing-II could penetrate 60m of soil before exploding and had a 1 kiloton, or even sub 1 kiloton, yeild. This low yield, and underground detonation with little (or no) radiation and limited fallout effects might lower the nuclear threshold, especially when striking a nuclear facility where some level of radiation leakage is to be expected. Military leaders might be encouraged to use the weapon, whereas they would be reluctant to use the larger yield nuclear weapons.

Another option would be a symbolic strike campaign at a nuclear site where the air defences are in a weakened state, such as Natanz. Damage would be minimal to none, but the purpose would be essentially saying that Israel can strike here.

I don't think Israel will go it alone on a strike on Iran's nuclear facilities however, options are too limited and they'd want US support for a protracted engagement. If anything, the option of symbolic strikes on Natanz is the most likely if Israel does decide to act.

The difference between Iran and Yemen is Iran has a more developed economy and military, and everyone knows where the key sites are located, key countervalue and counterforce targets, the nuclear facilities and missile cities, air defence sites and military bases and so forth. Yemen on the other hand is one of the poorest countries in the world, and aside from a few key well known countervalue targets like airports and seaports, and counterforce targets like the Amran tunnels, which the US and Israel did bomb extensively, there's very little intelligence on exactly where everything is. After that, it becomes a very expensive game of whack a mole. Trying to stop the launch of solid fueled ballistic missiles which can be wheeled out of a tunnel, tent or building anywhere in Yemen and fired in minutes is not feasible, it's just SCUD hunt 2.0. However Iran is also not prepared to fight like Yemen or endure what the Yemeni people have endured. Iran will stop fighting long before that. Iran has a lot more to lose than Yemen has.

There will be no preventing Operation True Promise III if Israel attack Iran, it would have to be weighed in any potential calculations. If Iran chooses countervalue targets as part of such an operation, the result would be devastating for Israel and Israel would likely respond in kind with countervalue strikes, instead of just strikes on nuclear facilities.

As for where Israel is currently, I don't think I can sugarcoat it. Hezbollah still hasn't carried out any military operations in months, even after the expiration of the ceasefire in Lebanon and Israel launching Gideon's Chariots. Syria is gone, led by ex AQ Al Jolani. The resistance operations carried out by Hamas, while brave, are not near what is needed to push back on Israel given the extent of what is planned under Gideon's Chariots. I think over two thirds to three quarters of Gaza is currently under IDF/IOF evacuation orders and Israel (with US PMCs) are the sole distributors of aid. The situation is bleak, Rafah essentially no longer exists anymore. I think this is why we see so much criticism of Israel from Europe, because now that they know the end result of Israel taking over Gaza is inevitable, they are free to criticize and speak as it won't change anything, in typical European virtue signalling and uselessness.

Iran has underground missile cities and nuke cities that are deeper and more sophisticated than anything in Gaza or Yemen. Anything less than nuclear weapons will not be able to destroy them. The channel I linked has a large selection of videos on various different missile cities that we know about. This one is about the Karkas centrifuge site.

The enemies needed how many bunker buster to assasinate Sayed Hassan Nasrallah? And his base in Dahiyeh was not even that deep, all things considered.

"Bombing nuclear sites" would actually mean bombing power plants, sanitation systems, and other infrastructure to attack the people, which is the same thing the empire has always done.

they could/would collapse entrances, nuclear facilities are not 1 man tunnel, i think it's feasible to do, cause structural unsoundness hits differently when it's a building/series of rooms with columns and stuff + dust entrance in some delicate manufacturing line fucks all of it. but further action depends on enjoying-spouse-infidelity level of iran itself (like the pro lib move would be to say "that's done than, invest in us, daddy"

hypothetically speaking, electromagnetic or laser assisted primo nuclear separation device is not that big (they can give pure u235, but veryyyyy slowly, less than gram a day). iran likely dismantled them (cause they are scary and are explicitly for weapon purpose), but still, they could make them again. think scientists isntreal merked ~10 years ago were roughly in that area, so isntreal seems convinced lately it's not a problem, maybe they are that infiltrated, maybe they are that reckless.

what's i'm saying is, any person with billion of dollars, vacuum pumps, lasers, copper and uranium can separate isotopes, it's a ridiculous pretense. they could do it with ~~a box of scraps~~ rinky dinky tech of 1943, it's miles easier now

So theoretically, the conventional way, the u.s military relies essentially on utilizing long-rage armaments launched by Sea-Air-Land outside of the maximum range of opfor forces to retaliate against which are then guided in by usaf stealth aircraft or special operations units penetrating the opfor defensive lines with the purpose of eliminating forward air defense networks and creating a more safer avenue of approach for conventional forces to penetrate.