There is probably a more elegant way to do this than I'll describe, but this method will work.
Code;Sprites spawned from Bubbles
org $02D9A1
db $0F,$0D,$15,$74 ;Goomba[$0F], Bob-omb[$OD], Cheep-Cheep[$15], Mushroom[$74]
;GFX Tiles used by sprites in Bubbles (2 animation frames with 2 bytes in them)
org $02D8A1
db $A8,$CA,$67,$24,$AA,$CC,$69,$24 ;Goomba[$A8|$AA], Bob-omb[$CA|$CC], Cheep-Cheep[$67|$69], Mushroom[$24|$24]
;Palette/GFX Page Table of Sprites in bubbles
org $02D8A9
db $84,$85,$05,$08 ;Goomba[$84], Bob-omb[$85], Cheep-Cheep[$05], Mushroom[$08]
;$84 = 1000 0100
;$85 = 1000 0101
;$05 = 0000 0101
;$08 = 0000 1000
This code is part of the default vanilla SMW bubble. What I provided for you is code that will enable you to change the sprite spawned when the bubble is popped, the GFX inside the bubble, and the bytes used to change the
YXPPCCCT of the bubbled sprites.
To achieve an empty bubble (replacing a goomba) you'll want to do the following:
Code;Sprites spawned from Bubbles
org $02D9A1
db $69,$0D,$15,$74 ;We changed Goomba[$0F], to Null sprite[$69]
;GFX Tiles used by sprites in Bubbles (2 animation frames with 2 bytes in them)
org $02D8A1
db $8A,$CA,$67,$24,$8A,$CC,$69,$24 ;We changed Goomba[$A8|$AA] to GFX tile [$8A] for both animations
;Palette/GFX Page Table of Sprites in bubbles
org $02D8A9
db $85,$85,$05,$08 ;We changed Goomba[$84] to use 2nd GFX page [$85]
Because the code above changed the GFX tile for the bubbled sprite to $8A, and $8A isn't exactly empty, use this
GFX02.bin replacement to make that tile empty (vanilla doesn't use the tile anyways so no other sprites will be affected).
As I said, there is probably a more elegant way to do this, but this method functions as desired. It will replace every goomba containing bubble with an empty one.
If you want to empty all 4 versions of the bubbles completely just do this:
Code;Sprites spawned from Bubbles
org $02D9A1
db $69,$69,$69,$69
;GFX Tiles used by sprites in Bubbles (2 animation frames with 2 bytes in them)
org $02D8A1
db $8A,$8A,$8A,$8A,$8A,$8A,$8A,$8A
;Palette/GFX Page Table of Sprites in bubbles
org $02D8A9
db $85,$85,$85,$85