There are plenty of plant sources of Omega 3. Flax seeds, walnuts, soybeans, and canola oil all have decent amounts of omega 3 in them. As for protein, legumes generally have a bunch.

Really, the only thing a vegan needs to supplement is B12, but even that gets added to a bunch of stuff like breakfast cereals and plant milks if you consume those.

You can take them as supplements. It's the same for your body. Oh and you are already doing that, because they give supplements to the animals they raise and kill, we are just eliminating the middleman.