My boy had the same problem. It basically becomes a spay instead of a neuter. My boy ended up with 3 incisions (not very long), one at his scrotum to get the normal testicle one in the crease of his leg and one near the base of his penis as they had to hunt. Yes it typically lengthens the time of the surgery (and thus will increase your bill it will not be a typical neuter bill), and the recovery is a bit longer (for us it was 7 days of ZERO activity and 7 days of minimal activity), but no long term effects at all. They should be neutered due to this though as leaving it will increase the chances of testicular cancer by leaps and bounds, but once the neuter is done no there is no long term issues. If you got your boy from a reputable breeder though you should inform them as it is a genetic condition and if they are decent breeders they will want to know. And no additional surgery. They remove the testicle same as they would if it was in the scrotum it's just hiding instead. My vet said she had one once that was a 3 hour surgery but she finally found it hiding behind the LIVER LoL. But no, once they have found it, no biggie and no long term issues whatsoever.
My boy had it done when he was 6 months, he'll be 2 years tomorrow and it's just a distant memory, nothing terrible at all for us.
Good luck!