If the shell can only be destroyed by a Shoryuken, then you know it's a bug.
Logically, that makes no sense. We already know that enemies in Megaman games have tolerances specified to each special weapon. In X1, the extreme end of this, and a very applicable example to this case, where the Hadouken cannot damage Final Sigma. It makes sense that the Shouryuken, as a weapon, has it's own tolerance variants against certain enemies.
I'd say the AI screw up is far better evidence that it wasn't intended. Though, the game doesn't crash at it's absence. I'd say it probably had been found out in testing, and decided to leave it in, but patched Snail to not crash when the shell disappeared. It's possible they patched it quick to not crash, instead of removing it, because it broke the Shouryuken move in it's entirety to 'truly' fix it. Their release schedules were extremely tight, and things like that are usually shoehorned in at the last minute. Plus it is a hilarious and well hidden event.