In the 2012 Toaplan STG Chronicle interview (released as a bundle alongside the Toaplan STG Chronicle music collection), the game's composer Tatsuya Uemura confirmed that Zero Wing was originally just a test project for new hires and that it wasn't meant to be released commercially. Mr. Uemura stated:

A line of dialogue was removed from the intro sequence in the English version. Said line translates as "thank you for you cooperation".

The game has 32 additional endings exclusive to the Japanese version. No official explanation has been given for the removal of these extra endings, but considering that they rely heavily on unusual speech patterns and pop culture references from the 60's and 70's, as well as the poor quality of the opening's translation (the source of the famous "all your base are belong to us" Internet meme), it's fair to assume that the localization team didn't translate the endings because it was possibly beyond their ability.