Well, the player and NPCs use the same definition for the ships. That means if you want to do changes for the player you also will do these changes to the NPCs.
An alternative to that would be to create completely new ships but that is more difficult than just changing a few ship stats.
The file you are looking for is the shiparch.ini located in \freelancer\data\ships\
There you can find all ships and their stats.
e.g. li_fighter would be the Startracker
under this entry you can change the hold_size or the hitpoints or whatever you want.
But like I said... it would also change it for all NPCs.
What you cant change there is the equipment of the ships. For the player ship there is a file called goods.ini (in the equipment folder) which has all data for that and for NPC there is a file called loadouts (in the ships folder).
For the changes on the wings you also have to edit the shiparch.ini.
Ships with wings have sections called "[CollisionGroup]". It is possible to change hitpoints there.
To identify the ships you can use FLdev.
You can enter the ids_name of a ship from the shiparch and it will display the name.