I don't know about the time-frame but, yes there where and there are musicman basses being sold with no case.
For normal production the case is included, because that's what they use for shipping. but there where times when sr basses where offered without case. also it is possible (but I don't know for sure) that some music stores sell the cases separately.
I bought my first 'New' Stingray in '99 and it did not come with a case... at least that's what the guys at Guitar Center told me at the time. The bass was on sale and under $1000 (that'll never happen again!) so I splurged and bought an SBK case for another $150. It was the only case they had that fit the Stingray, but I always wished for one that had the Music Man logo on it.
... I wish I still had that bass!
My '89 Ray came with a gigbag only. I bought it in '91 for almost 2000 DM and the bag was another 135 DM. Maybe I was offered a case but had no (more) money. However, the bag is original MM and after 25 years still in perfect shape.
It was my first good instrument and is still my favorite one