They may be an entry point for water and dust yet my current 3.5mm jack equipped Xcover 6 Pro is IP68 rated at 1.5m of water for 35 minutes according to GSMArena. I'm not exactly looking to go snorkeling with my phone any time soon either so it's not like it'll be a concern for anyone in the vast majority of use cases. I've had water splash on it occasionally over the years and it never caused any harm either.

I can't really talk about what the PCB footprint of a 3.5mm jack is but if it's something that already comfortably existed on most previous phones along with micro SD and Sim card holders until very recently then I doubt it actually matters. Keep in mind phone manufacturers are incentivized to hold back on as many features as possible if it means they can cut down on BOM costs and make an additional sale through apps or accessories down the line.