Hmm, I don't think you can get rid of a weapon, but you should be able to add them like with starbases.

As for purchasable upgrades, you probably could make an ability cost resources that then gives that unit a stat buff. It might take some work to get the AI to use it right though, but if that's not a concern it should be possible.

Are you talking about upgrade meshes?  Take the humble heavy TEC cruiser, make 2 upgrade meshes -1 gives side laser cannons and the other is a top missile rack?  That sort of thing?  You'd need 2 researches that "improve" the cruiser -1 laser cannons and the other missile rack.  those meshes could have hardpoints for the weapons, but you'd still have to figure out how to get the entity file worked out.  They could have ability hardpoints instead of weapons -ability for laser blast and ability for missile swarm so they appear to come out of the mesh at the right location.

Or, you could alter the humble cobalt mesh to have additional ability points where you want the laser blast to come from, then ability that can only be unlocked after researching it.  Then your cobalt has the ability "Laser shot" or "Particle Cannon" and it 'fires' from that ability point.