Just summarizing:
-your son is a pretty good player and is happy with the skates he is in
-his skating coach previously recommended new skates because he were getting soft but nothing about the fact that it was impacting his skating
-his game seemed to improve after that but there was no way to attribute that to new skates
-you notice that the top of his skates are getting soft when you squeeze them (which honestly may have little correlation to how they are affecting his skating once on his foot and laced, even down an eyelet) but are simply worried it will affect his performance
Seems like there is nothing to see here, performance should be the indicator as well as player preference.