with all the money they are making off of lockboxes they could get a ton of 3Terrabite External Harddrives and extend the capabilities of the server.
Please, if you do not know much about computer science, please do not propose fixes for problems you do not understand.
Most likely, the ships do not take up much memory and storage capacity is not an issue. It surely has something to do with limitations or bugs in the code which cause excessive computational cycles, memory leaks, or some such problem that leads to lag or instability.
It is really something they should fix, but they have limited resources and so long as the game is generally working (perhaps less than 1 in 1000 players get anywhere near the ship limit) they probably want to use their programmers to address critical bugs or develop new features.
Actually I understand quite a bit of computer science. Also if the code is so limited. it shouldn't be using the Champions Host. Perhaps something new. Something seperate from Champions and Neverwinter.