Acronyms and abbreviations are different things though.
Initialisms are pronounced by saying each letter in order. Acronyms are pronounced as if they were words.
"ID" is a funny case because it's an ordinary abbreviation, and not really an initialism* or acronym, but it's pronounced just like an initialism. I think I'd prefer it "ID".
I would definitely avoid writing it "Id", lest it be confused with Freud's concept.
* unless as Norm Macdonald joked, the "D" is short for "dentification"