Why was the Whelk's ability to hide in shell removed?

Similar to say... Brock's onix in the original pokemon games that used Bide, the Whelk used to be able to hide in its shell meaning any queued attacks that popped off after the Whelk used the "hide in shell" ability would try to find a new target(the shell) and then you would take the retaliation attack/KO.

What's the deal with removing this signature ability?

How can I put it back in....need to learn how to decompile snes roms... 

AFAIK it was a design decision. The original purpose (in unmodded FFVI) of the shell mechanic was to help familiarize the player with the ATB system. I think the logic was that since players are plenty familiar with that system now, it was a pointless mechanic to reinforce in this way. It now serves, in my opinion, as a tonal message to players of the mod that they can no longer rely on busted mechanics present in the original. I think BTB has addressed this specifically in the past, but too lazy to find where.

It's more that the fight is too short to really illustrate much about the combat system.  Now it's just a small "are you paying attention" test and on to the rest of the game.

It's worth noting that there is limited space for enemy scripting, and that BTB filled every byte of it for the 2.0 release. Whelk being part of the intro, it was deemed unimportant to dedicate valuable AI bank to him, so he kinda just became "press A to win".

There has been a lot of discussion about Whelk's neutering on the BNW Discord channel. Some people feel that if he's such a pushover, it would be better to just rip him out entirely.

Since the 2.0 release, some AI fixes have freed up a modicum of space, and a happy medium has been struck for the 2.1 release where Whelk will start the battle in his shell, so the player still has to pay a bit of attention instead of just "press A to win". Still a pushover because intro, but the spirit of his gimmick lives on.