You're right on both counts; you can give an outfit up to four effects, but the Nova engine will only acknowledge the Weapon or Ammunition effect if it's in the first of the four slots, hence MC only lets you put it there.
What you'll need to do is make several different bays. Say bays 128, 129, and 130. Then, make bays 129 and 130 invisible (so give them 9999 tech level and check "cannot be sold.") Finally, put the following string into the On Purchase field for Bay 128: "g128 g129 g130" (sans the quotation marks). What this does is tell Nova that when you buy bay 128, you should also make it give the player bays 129 and 130. You also have to tell it to grant itself because of a bug in the engine. Then, put the string "d128 d129 d130" in the On Sell field, which means that when you sell 128, it will delete all 3.
Now, the only time that you may run into trouble is in something like the following scenario: I buy 2 bays, fill bays 129 and 130 with fighters, then sell one of the bays. I now have two times the number of fighters for bays 129 and 130 that I should be able to own. Nova will let this happen without giving the "you must sell X more fighters before you can sell this bay" because you're not really selling bays 129 and 130; they're just being deleted. For that reason, to ensure the bays won't be exploited, you should make bay 128 also delete a number of fighters for bays 129 and 130 equal to the number of fighters a ship can hold per bay. So if I can hold 4 of fighter 131 per bay 129 I own and 3 of fighter 132 per bay 130, then you should add "d131 d131 d131 d131 d132 d132 d132" to the On Sell field for bay 129.
I know that may sound a bit confusing, but it's quite simple once you get the hang of it.