The bombchu is NOT using a super bomb as a weapon. It is using bomb (from default). However, the blast is Just big again and that happens only when the Bombchu hits Link.
Bombchu is using large blasts again. [798]
The bombchu originally used the super bomb (large explosion) in close proximity to Link when it was first added to the enemy list. It only uses the normal bomb when Link kills it.
Read Misc Attribute 2 for the Rope Enemy Class:
Misc2: If Misc1 is 1, specifies the weapon to use when in close proximity to Link. This value is treated as an offset which is added to the enemy's ordinary weapon to obtain the proximity weapon.