You're talking about flights in from abroad being cheaper, right? That may be different from the situation within the country. Yes, cherry blossom viewing is very popular here, but the first week of May is the huge national holiday of Golden Week, when people travel, so they may just be waiting until then, and airlines may just be adjusting rates accordingly.
I also read that tourism is down 40%, so perhaps airlines that you saw were trying to get more people to visit.
Oh, and cherry blossoms bloom over a wide range of dates here. Where I live, we won't see them until May.