That might be because of the NYGM damage mod - intitially, this ship was designed with 2160 HPs to be compatible with this mod. I assume you are using the Beta (1.0). Download version 1.1 from my signature - there are two .zon files, one with 2160 and one with 200 or 250 (I don't remember). If you do have 1.1, you are probably using the NYGM .zon file (check the readme for more details).
Version 1.0 of the Whale Factory had only the low HPs, actually. Version 1.1 has both.
