A super missile counts as two projectiles. When the graphic projectile dies, it deletes all super missiles. ALL.
So, if you have two super missiles on screen, the moment either one dies, the other one dies as well (give or take a frame).
This is really stupid, especially considering that the routine to delete the multiple super missiles is less efficient than using the graphic projectile's link to the super missile.
So I made use of just that. This code (should) allow you to fire multiple super missiles without worrying about them being deleted when they shouldn't be. Also, this fix exists entirely within original code; no extra space is used, so unless you tweaked this specific code, it should run fine on any hack.
Of course, you'll probably want the easier-to-use ips patch for headerless roms.

90:ADB7
	PHP
	REP #$30
	STZ $0B64, X
	STZ $0B78, X
	STZ $0B8C, X
	STZ $0BA0, X
	STZ $0C04, X
	STZ $0BF0, X
	STZ $0BB4, X
	STZ $0BC8, X
	STZ $0C18, X
	STZ $0C2C, X
	STZ $0C40, X
	STZ $0C54, X
	STZ $0BDC, X
	STZ $0CB8, X
	LDA #$B169
	STA $0C68, X
	CPX #$000A
	BPL BRANCH_ALPHA
	DEC $0CCE
	BPL BRANCH_BETA
	STZ $0CCE
	BRA BRANCH_BETA
BRANCH_ALPHA:
	DEC $0CD2
	BPL BRANCH_BETA
	STZ $0CD2
BRANCH_BETA:
	JMP $B02B

08C2309E640B9E780B9E8C0B9EA00B9E040C9EF00B9EB40B9EC80B9E180C9E2C0C9E400C9E540C9EDC0B9EB80CA969B19D680CE00A00100ACECE0C100D9CCE0C8008CED20C10039CD20C4C2BB0


90:B02B
	LDA $0C7C, X
	STZ $0C7C, X
	PLP
	RTL

BD7C0C9E7C0C286B


90:B01B
	AND #$00FF
	TAX
	JSL $90ADB7
	RTL

29FF00AA22B7AD906B