Most likely I would try to dance around it or find a different way to convey my thoughts (like for any other thing I couldn't express clearly) or use `it` because in my first language (french) `il` is the default pronoun for a baby (`il a faim ton bébé ?`) while thinking something's off and ask the person to forgive my blunder.

I would certainly not used something like `is they a boy ?` though.

In english there are two ways to refer to a person of unknown gender. "it" and "they". Of a baby you could say:

"Is it a boy or a girl?" or "Are they are a boy or a girl?"

Both are perfectly correct and common, but "it" sounds impersonal and as such can be a bit rude.

I have never heard anyone ask "Is they a boy or a girl?".

This is actually a problem for me. I can't see the difference between pink and blue baby clothes.

I'd just ask the name, that should be a strong clue. If not then wait for someone to talk to or about the child.