It really depends on what happened to your son. If there was just touching then there will be no evidence. If there was forced penetration (sorry if this is rough to hear) there might be some evidence of that still.Will the Dr. Know if he has been abused even if it has been a while?
I'm basing this off my time as a victim advocate and sexual assault response coordinator in the military and the training we got to do those roles. I know that evidence like fluids is gone within 72 hours. Physical evidence may remain. If it only happened once it's iffy.
If the doctor finds anything, you report it. Immediately. You tell the police your son identified his father as the one who did it. You let them investigate.
It's quite possible if he was molested that someone else did it and coached him to say his father. Or it's possible his father could have done it. No one is going to know for sure what happened until it's investigated. But based on my experience with sexual assault cases that weren't reported for weeks or months, they are very hard to investigate. I had a victim who said she was sexually assaulted by the alleged perpetrator forcing himself in her mouth while she slept. But she waited about three weeks to report it. The civilian cops barely investigated and dismissed it. Then CID took it and after two months said unsubstantiated - not that it didn't happen. They just couldn't find enough evidence to push forward. I had to tell that soldier that and she was devastated.
The bottomline is that you need to report it now. Because if you keep withholding visitation and you never report it and then he takes you to court for contempt of the visitation order, and then you bring t up, the judge is going to not be happy. Will likely rule make up time for your ex.
Take care of your kid and get to the bottom of this.