WhatsApp and Instagram similarly serve more users per employee than Signal does, at an average compensation lower than what the average Signal employee makes.
It's interesting if their headcounts are similar, although maybe not entirely unexpected. It doesn't take that many people to maintain a messaging service, so there shouldn't be that much of a difference.
If I'm being generous to Signal, I could say that most of the extra employees at these companies (e.g. Facebook) don't directly work on Messenger itself, but work on the surrounding data collection/ad tech. At the same time, there is a certain number of employees that any company needs just for people to handle the administrative/business side of things, so that explains the extra people working for Signal.
If I'm being less generous, maybe Signal really isn't that different, and Facebook et al just have so many extra people because they are liable when it comes to content being posted on their services. For example they need extra lawyers and content moderators to handle all the stuff that is publicly posted on Facebook. This is something Signal just doesn't have to deal with.
This is all just speculation though, I don't have any numbers that indicate which is true.
Instagram had 13 employees with 31 million users when it was acquired by Facebook.
I don't know what the post-layoff employee account is for Meta Messenger as they did not disclose it in their SEC filings, but pre-layoffs it was several hundred.