I'm pretty sure I know the answer to this question but just making sure, can you make modifications to a ship like increasing its hull or hyperdrive?

No. There are modified ships that exist, but they are mostly gifts/prizes from the admins. Others are simply old ships, which have since been changed.

That's quite simply a no. Perhaps much later in the future that will be possible.

Most of the modded ships you see now are from Red Scenarios (like the WS, except if you die in the RS, you die for real). Nobody is sure if modifications will be included when R&D is released. I wouldn't hold your breath for R&D either, as it will be quite a while before that is released.