An entry fee isn't unheard of for reputable contests that have actual cash prizes. They're awarding a total of 13,000 in cash [1,000 for each first place winner and 3,000 fr the grand prize winner] plus the gift certificates, plus whatever arrangements need to be made with the other magazines for things like guaranteed reviews, etc. If they get 130 submissions their cash prize is covered.
It's also possible they have to pay judges and whoever else works on the contest as staff - reading 130 novels? That's a lot of work. I've read an article by someone who judged a reputable national novel contest, and it exhausted her - I think she had a month to go through several hundred submissions while still doing whatever job she had and also, well, writing.
I'm used to entry fees in professional contests, such as graphic design awards run by different associations or schools. The entry fees ran $25 for the first piece and $10 for every additional, if you were a student. That was back in 1999. The fees paid for the contest's overhead as well as judging.
Another very important thing entry fees do is cull down the number of submissions to something reasonable. The amount of people who have self-published a novel, or even just want to submit something that doesn't fall within the contest guidelines? Quite a few. The amount of people who are willing to risk $100 on the possibility that they have what it takes to win? Significantly less. Just think of the reduced amount of mail they have to sort by charging an entry fee.
(It's sort of like when someone advertises they're giving away a pet, and they attach an 'adoption fee' to it. Usually the fee goes to something like food or spaying the animal, but what it really does is help ensure that whoever adopts the pet is serious about it, and reduce the number of people running to their door for a free pet.)
There's even journals and magazines that require a small fee upon submission for much the same reasons. This isn't the first contest I've seen that's charged an entry fee of this size and wasn't a scam. I think it's a little high but not unreasonable. I'm not sure if I'd do it, personally - only if I had a very good published paper novel to submit, and I was doing pretty well on the money front and could spare that $100 without flinching. (Haha, neither.)
But yeah, it doesn't have the same hallmarks as writing scams I've seen online like www.poetry.com. A poet friend's mom submitted her stuff for one of these [without her knowledge, or my friend would have told her mom it was a scam] and ended up paying I think $60 for a book that had her poem printed in it with about a thousand other 'winners'. They advertise their contest as free, because what they really want to do is hook you for the vanity publishing scheme. There's a whole group of poetry 'contests' like that, with the bait and switch technique.