Looks like it's unconfirmed but likely it was specifically named for monosodium glutamate. "This is where we keep the tasty content."
https://en.wikifur.com/wiki/E621
https://www.dictionary.com/e/slang/e621/
https://knowyourmeme.com/memes/sites/e621
(Edit: Apparently there's a sister site called E926 to share SFW content. E926 is yet another food additive (Chlorine Dioxide) which is used to bleach food for a cleaner appearance.)