It's up to you. They stack.
I know a lot of people are asking for upgrades to be separated from inventory, but basically it's a balance of how much cargo space you want versus your tech.
I imagine on my PS4 fighter I would eventually have a lot of slots but not actually be using any of them for cargo, so that it could be as strong as possible. That's assuming materials collected in space will go into your exosuit inventory, I thiiiink they will but I'm planetbound at the moment.
They don't. It will say that the ship inventory is full and then nothing can be collected while in space.