Hi Shade, welcome!
OK, here`s how you can take out specific ships atm:
1. You make a list of the in-game names of the ships you want to remove from the game.
2. You open the Realistic Shipyard`s shipdata.plist and search via search function after those names.
3. At each name, you write down the plist name: It´s at the beginning of each shipdata & shipyard.plist entry and says "<key>shipname</key>". Write down those plist names also.
4. Delete the entries of the ships you don`t want in the shipdata.plist. Keep in mind that many ships have different versions, some player and some NPC, and if you want them completely gone, you have to take all of them out. You should already have found them all in step 2. Don`t forget to erase their subentities, too!
5. After editing (and saving) the shipdata.plist, open the shipyard.plist.
6. Search for the plist names of the player versions of the ships you want to remove (you won`t find their in-game names here).
7. Remove the entries corresponding to the ships you don`t want.
8. Save your new shipyard.plist.
9. Next time you start the game, remember to press SHIFT while starting so that the game recognises the changes you have made. After that, at every game start you have the oxp without the ships you don`t want.
At the moment, there is no installer/deinstaller for specific ships. Some people said they would create something like that, and while I`m looking forward to that, it has not yet happened, and I can`t (and, frankly, don`t want to) do it myself.
So, only way to remove specific ships, is to do it manually the way described above.
Anyways, have fun with Oolite, cheers
L