Does Maynard always say "see you soon" at concerts?

Danny: “new album coming soon “

Pretty much. 

Soon is a relative term

No. Some times he says, “whelp, you’re still here”.

Yep

Wouldn’t read too much into it, I saw APC in 2000 in Halifax NS and at the end Maynard said “we’ll see you again soon … one way or the other” which people took as a confirmation that Tool were coming which never happened

I think he says it in a spiritual sense.

Only when he’s going to come back to that place soon.