@smwln: Part of the requested patch already exists in form of the
star coin patch.
There is also the
overworld counters patch which is once again that what you have requested.
Don't forget about
SRAM Plus which saves them generally.
The only exceptions are about the Yoshi wing bonus level but considering that the star coin patch uses custom blocks, you have to edit the blocks itself and that there is no option that the game doesn't remind the collected dragon coins so you have to edit the patch but still, you request already existing stuff.
However, I still can fullify your request partly about the vanilla dragon coins in the bonus game:
Codeorg $00F34E
autoclean JML bonus_level
bonus_level:
LDA $1B95
BEQ .return
LDA $13BF
LSR #3
TAY
LDA $13BF
AND #$07
TAX
LDA $05B35B,x
ORA $1F2F,y
STA $1F2F,y
.return
JML $00F357
You can also put
STZ $1422 : STZ $1420 into the level init code for the Yoshi bonus level in UberASM to clear all collected dragon coins and use Map16 tiles (once again, if you use default dragon coins).