The mosques were in the buffer zone that Egypt is building to curb illegal smuggling tunnels to Gaza. Clearly, the Egyptian government believed that Hamas would have no problem using mosques as entrances to the tunnels to smuggle weapons - in either direction.
What? You mean you didn't hear about the destruction of three mosques? Funny how that happens.
While Al Jazeera says that this caused a furor, I am not seeing anything about it in other media. Egypt has jailed some Al Jazeera journalists, and AJ is not a fan of the regime, so it likes to make it look bad.