The HP bonus is fine compared to having exp improve a ships attack or defense. This would be even more imbalancing.
I'm still not convinced for the issue with HP bonuses. It just doesn't make sense to me. The crew gain experience and what? Do the crew members attach themselves to the ship structure to make it harder?

I would rather say they learn how to use their weapons, shields, even engine effectivelly. Unbalancing the game depends rather on the size of this bonuses. If it's just for example 5% of the ship attack value for for each level, then I don't know how you can find it 'unbalancing'. You would need 10 levels to get 50% increase, which I think is OK. It could even be 2% if 5 is too much...
And BTW one of my ships on 9th level tripled his HP points, isn't it too much?
Changing the game to allow you to use your starport to upgrade an orbiting ship? Hmm, I don't really see a need for this. Trying to choose your ship upgrades wisely and managing your money are important to the game.
Why not? Starport is a facility where ships part are built, they are next lunched to the orbit and the ship is assembled, why we cannot upgrade already orbiting ships by replacing some modules? It seems logical to me...