Deposits aren't that unusual...I've paid deposits for the two custom cues I had made by two different cue makers, one of them highly regarded. If he's got to special order a big piece of something like Abalone or MOP or something unusual, or a hard to get wood and then starts on your cue, it might be hard to sell to someone else unless they order it very close to the way you did. There are some with a reputation of taking the deposit then never getting around to making the cue, just do a search. Jerry Rauenzahn made me a cue to my specs with 100 year old Brazilian rosewood and a HUGE wedge of abalone he had to special order...so asking me for a modest deposit was no biggie to me at all. I'd say if you go with one of the more respected makers and they ask for a deposit, go for it.
To answer your original question, I'd say about 10% - 15% ($200-$500?) would be more than reasonable, and if he wanted more, would depend on what you're asking him to do and the reputation of the maker.