I've found this aspect of the game fairly annoying.
I've never rolled a refit in all the months I've played SH4 since it was released, at least not that I can remember! Hence I've never had a tower refit! I believe there is a way to manually edit the tower that your sub is fitted with.
But its still a bit of an immersion killer when you're still cruising around in 1943 with that ruddy great 'bathtub' following you about when your on the bridge.
I hope this is something they will fix in the new patch and expansion.
IMHO they should dump the random element and just make it simple. A new tower uprade becomes avialable; the next time you dock back at base you automatically get it.