Yup, levels 5 and 7 but in level 5 I think it is, you have to bomb one of the walls to gain access to the room, and in level 7 theres just a doorway leading up into into from the right side of the map i believe (beat this game in 2 hours on sunday)
In lvl 4 the bomb room has no doorways and the walls can't be bombed to create openings. And just like Link had to walk through a wall in level 2 to get the whistle the same technique is needed here.
Lvl 8: the bomb room here is located in a devious manner and off the beaten path. Once Link reaches the room next to the 3 Dodongos guarding the triforce piece the bomb upgrade room is located four rooms in the opposite direction. More specifically bomb the south wall and head south.