well you can't add a weapon, because number of weapon slots is limited, but it is possible to exchange a weapon with simple hex editing. I actually exchanged the UUV in the akula with mobile decoys, so like in real life my akula carries the mobile decoys in her external tubes. There is one Problem though, I still have to find out how to exchange the weapon settings screen. for exampe if you exchange harpoon with TLAM, the weapon screen would be the one from the harpoon not the TLAM, so you can't add waypoints. It is possible to do it, the RA mod team have done this, It is very possible that only wpnloadout.dll is involved, but I don't know how to do it.
to exchange a weapon you need DWedit and a Hexeditor.
I use HxD since you can enter integer numbers with it and it is freeware.
First you need the entinity numbers of the wpn you want to replace and the one you want. for example I want to exchange exhange uset-80 () withe ugst. open wpnloadout.dll with hxd, go to replace, set to integer number, search for 1631 (uset )replace with 1396 (ugst). normaly occurence about 10 if more than twenty you may risk to **** up your dll, may try and error to find out wich offset essential for wpnloadout. after Hexediting go to DWEdit, go to Launcher Dialog, find Launcher of your sub, and change something of the loadout. then start DW choose a mission and go to wpnloadout screen, you will you have new weapn.
If you want to use HxD you can get it Here:
http://mh-nexus.de/en/hxd/