Is there a limit to the number of items a ship can carry?

[Machelvanius]

It is because of this limitation that most equipment vendors that specialize in code weapons now use bases for selling those code weapons, or they sell them to bases. The 100 individual item limit is part of the original code of the game, and probably can't be changed, although I'm not one of the coders. Keep in mind, you do not need to keep the items on your ship to have them in your neural net.
In fact, that's a bit counter-productive.