This is interesting to me as some use the game situation to decide if they "notice" the coach asking for one they don't have (Ref in PA) and others would seem to grant the TO regardless (Juggling). I apologize if I mispoke for you two, but that's what I got from your posts. (With the exception of Juggling paying more attention to the floor as to not miss anything.
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Again, you also have to decide if you're going to be the official who tells the coaches they have none left or the official who says, "Hey, they've got assistants. It's not my job." I lean toward the side of telling the coaches, but... My main concern is that I don't want to get bad info. (perhaps less likely at higher levels, but still...) and pass it on to the coach. Then, after I told him/her, "You've got one left!" they call it to find out they don't.
I wonder if informing them by saying, "The scorekeeper has you with 1 timeout. You can check it," relieves any responsibility on the refs (my) part. I don't want to be obsessive about it...but I also don't want to be part of a mess that I could have avoided somehow.
Thanks for the thoughts.