Oh, definitely.
Three ways.
Way #1: Semi-complicated. You can give them the exact same name as an existing model (aka delete the Akira folder in the models folder, then rename the folder of the mod to Akira, and the modnameBS.bmp to AkiraBS.bmp, modnameTI.bmp to AkiraTI.bmp, modname VL.bmp to AkiraVL.bmp, modname.mod to Akira.mod, and modname.gf to Akira.gf). You will see the new model in place of another ship. You can still play on the dyna.
Way #2: Semi-easy.
Drop the model and its folder in the models folder. Go to SFC3\Assets\Specs and open DefaultLoadOut.txt in Microsoft Excel, or OpenOffice (free). Find the ship you want to change (say, replacing Akira with modname), find the column where the model's name goes, and change it from Akira to the mod you want it to be. Close and save the file, ignoring the little popup warnings and overwriting the original.
Note that if your core files such as DefaultLoadOut and DefaultCore are different, you will not be able to play multiplayer Skirmish. I think you can still play dyna servers as long as DefaultCore stays the same because you'll use the server's loadout.
Way #3: Complicated, but best.
Create your own line in DefaultCore.txt, following the others, and create a line in DefaultLoadOut, that matches up with the line in DefaultCore. You can create your own ship with whatever specs you want to give it this way, and theres tutorials for doing this. This is what the modders have to do, and this is what you have to do if you want non-stock ship weapons load out.
I'd recommend downloading CoreEdit, but it doesn't work with the new patch.