It literally ishttps://books.google.com/ngrams/graph?content=happy+as+a+clam&year_start=1800&year_end=2022&corpus=en&smoothing=3&case_insensitive=true
Those are very small percentages. Maybe it is a phrase some people use, I'll accept that, but it is not common.Compare with an actually common expression
I always assumed it's because clams look like a pussy, somewhat.
With the crack and all that.