Fred2 gave space for 3 primaries and 4 secondaries for non-player ships.  If this has been expanded beyond that, I know nothing about it.  It would mean some changes have to be made in Fred, too.  
Personally, I don't think the primaries should be expanded beyond 3 apparent banks -- it just gets too messy, not to mention ridiculously overpowered as far as play balance goes.  For that matter, I should think four secondary banks ought to be more than enough for any one bomber for any one mission.  I mean, five banks?  One could put some of 
everything in there!  Good missions make Alpha 1 not be a one man show; having five secondary banks would work counter to that. 

