As already mentioned, Sandro discussed this on the Q&A and yes, there's a technical reason. It's a tad lame but basically I think it comes down to the fact that, because the UI currently presents stored modules in a long flat list, scrolling down a list of a 1000 modules would be impractical. Basically (and this applies to bookmarks and friends lists and group management and any potentially long lists of data), you need, at the very least, to implement some sort of folder structure (or better still a named/categorised/keyworded faceted search facility) if you're going to do this "properly". Since FD are too busy to do this "properly" at the moment (and hey, I understand what that's like) the quick solution is a flat list and a limit on the number of entries.
While I understand the reason for this, it still is kind of a moot point when you consider that before 2.1, outfitting an optional internal slot gave you a long, long list of every single possible class and rating of every optional internal, all in one big list.
I can only imagine what fitting a class 8 internal at Jameson Memorial must have been like.
Still, since the module storage limit is account-wide and not per-station, I'd much prefer a far higher number, or the ability to pay credits to increase the cap as much as I like.
If long lists are an issue, simply add "pages" like exploration data has, and problem solved.