Instead of saying "You there?" I would prefer "You have 5 minutes to discuss X?" or "Do you have a moment to hop on a call to chat about ?". That way I can make a decision on if I have time for it or not, instead of having to reply with "I'm here, what do you need?" only for it to end up being something that I didn't want to be disturbed for.
The people that I would send a "you there?" message understand that my message is shorthand for that. They might respond with "in a meeting" or "gimme a few minutes" or if they are available for a synchronous conversation, "hey" or "what's up?"
I have a couple contacts that are "on the spectrum" and I deal with them a little differently. They seem to need things spelled out a bit more explicitly. But those people tend to get left out of many discussions, and don't seem to do as well careerwise in the long term, because they don't really connect on a human level with people.
However, there are people who I work closely with who understand that if I do some sort of "are you there?" it's because I want to have a fairly synchronous conversation over the phone or over chat.