Boys will mark more when they are not neutered, but now that he is older and might be used to the behavior, just fixing him may not stop the marking altogether. We had this problem with our male yorkie.
Housetraining is not usually something that happens quickly/easily; it can take lots of time and patience and especially watchfulness.
Every time they have an accident, they are getting used to that kind of behavior and it "detrains" them just a little bit.
So, to answer your question, yes it definitely does happen and 6 months is not unheard of.
IMO, if you need to get him trained in order to keep him, it's going to take some time, dedication and lots of positive praise on your end to get it done.
There are some great resources on here for potty training -- a search using the search option at the top will lead you to tons of threads with advice too!
If you'd like a couple more specific answers:
1. How long is he in the crate for during the day?
2. Does he hold it in the crate all day?
3. Does he have free run of the house other than being in the crate?
4. What techniques are you currently using to get him to use the pee pads?
Good luck, and I'll give you some more tips when I know some more info
