When this was mentioned in NB 13 it was very subtle ... and Blair's EQ works are not exactly famous for being subtle. In case it was implied elsewhere I never noticed.
Like you I'm pretty sure that Bowki was aware that something bothered his father, Startear. Not all the time - Dart obviously had happy and proud times with his son. But he noticed most probably ... even very young children "sense" when something is wrong without actually getting the reason.
Bowki had Talmah as a second Dad ... may not be a big matter for him during his childhood. But a father who went in wrapstuff ... would be only natural when Bowki asked questions sooner or later. And the Go-Back attack together with the vulcano eruption was a topic among the villages for sure - even years later.