I saw this loop in Rockman 3's reset code (not sure if Mega Man 3 has it, but it probably will). As far as I know only the first two writes to $2006 after reading $2002 have any significant results. The EOR in the loop is also a bit odd. It would write #$00 every other loop and #$10 on the others, but it still doesn't have any significant meaning what the loop is supposed to achieve.
I'm not sure if the second write to $2006 resets the latch similar to reading $2002, but according to FCEUX it does since the PPU address changes between $0000 and $1010.
EDIT: I should also add that there are no writes to $2007 anywhere near this loop
Code:
LDA $2002
LDA #$10
TAY
Loop:
STA $2006
STA $2006
EOR #$10
DEY
BNE Loop
LDA #$10
TAY
Loop:
STA $2006
STA $2006
EOR #$10
DEY
BNE Loop
I'm not sure if the second write to $2006 resets the latch similar to reading $2002, but according to FCEUX it does since the PPU address changes between $0000 and $1010.
EDIT: I should also add that there are no writes to $2007 anywhere near this loop