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Any thoughts why his father wouldn’t want to see him?

Hopefully it's shame or embarrassment but judging from the type of person he was I rather doubt that's the case. Perhaps it's payback. "Ignore me for 20 years...I want noting to do with you." I'm sure we're going to find out.

I think his father is probably still a little angry with him for not even finding out if he was lost in the hurricane or not.

I can see why Dan wouldn't welcome him with open arms after being ignored for 20-odd years.

After Will left him once, he’s probably hesitant to have contact with him at a point when Will would have the superior position

Even if they have a poor relationship it must be pretty embarrassing to have any sort of reunion in prison.

His father has cut him off after all these years and you can see why if there was no contact in 20+ years.