I've search a bit and the closest thing I found was this thread:
http://fractalsoftworks.com/forum/index.php?topic=1785.0. If this has already been mentioned I apologize, I've been out of the loop for quite some time.
The idea I have is similar to the one mentioned in the thread linked above, with the exception that we're not simply talking about switching out ammunition and such. The thing I want to focus on is the refit time of weapons. Since we can refit on the fly, it seems to me that instead of all weapons, weapons of the same class, or refit time being made dependent on the class of the ship, certain weapon types like missiles and small simple ballistic weapons could be switched out for other missiles or simple or similar ballistic weapons respectively. This would add a strategic pre-planning dimension to the weapons you select.
For example, a missile rack switching out Harpoon for salamanders when facing a highly mobile but weakly armored threat quickly or instantaneously on the system map. Large and powerful weapons should take a long time to install and uninstall, and maybe instill a hefty speed penalty too to accentuate the differences of ready to fire missiles and weapons of similar make from big honking space guns that take a lot of pampering).