Not just once, but a whole lot; not just in his thoughts, but to Tim's face.
As far as I can tell, Dick's never done that anywhere else -- with one exception, and that was also written by Grayson, during the whole Tarantula/Blockbuster thing, and occurred immediately after a building had partially collapsed on Tim, whom Dick feared might be dead. ("Timmy, please...") It rang false for me there, too. It's worse in #110.
Here's why: guys don't do that.
You do not fuck with a guy's name. Unless you are being an asshole, whether serious or genial. For general use, you use his name or common nickname and go with it. You don't use variations on it, unless you are kidding around or trying to provoke a fight.
This is particularly true of diminutives. Such as, for example, "Timmy." That's something you'd call a child. It is not a name you would use to a teenage male during a heartfelt conversation, even if his name happens to be Timothy and especially if he commonly goes by Tim. Unless you want to be really, really condescending and insulting.
The only circumstance in which it is permissible to call a sixteen-year-old boy who goes by Tim "Timmy" is if you're hanging out and you're insulting each other lovingly, as guys do. Not during a serious talk. Or even a casual one.
A little thing. But it really bugs me.