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:

"This title was created as a training project for our new hires. At that time we didn’t have any plans to release it commercially. But the decision to release it commercially made it a much more practical learning experience for the new developers, I think. On the other hand, the stage design and characters were rather cobbled together, so the world of the game was kind of a mess."
Contributed by ZpaceJ0ck0