I think it was crystal clear that the reason he didn't tell Nathan the truth was because he didn't want Nathan to get involved in his mess. Alex had already considered telling Nathan the truth but that would involve Nathan even more. Alex doesn't want to trouble him, much more his family.
If one truly loves a person, he won't want to be the reason for the other's downfall.
Communication is a word easier said than done. It's not like Nathan was a powerful figure.

all he had to do was tell nathan that he was being blackmailed and that he was gonna date that twink. like fuck it’s not hard to communicateeeee lord.