Actually I would think that it would be impossible for malware to effect your brain even if you had an implanted comlink. The rules for malware state that technomancers are not effected and since technomancers essentially use their brains to hack, it would be the same if you used an implant.
No, it would absolutely not be the same.
For one, Technomancers can't have malware put into their head, because their
biological node does not use computer programs at all.
For two: IC-like malware would work the same way actual IC works:
by suborning your simsense module. ("Suborning" means "taking over by deceptive means".) That module - indeed, your whole comlink,
IMPLANTED OR NOT - would no longe be responding to your own commands. The malware would be in control, and it could do nasty, nasty things to you.
And in fact, there
is a by-the-book, RAW example of malware that uses black IC:
DeathwormsDeathworms are IC-like weapons designed to knock users offline or even stun/kill hot sim VR users.
Programs: Attack, Black Hammer or Black Night, Exploit, Stealth
Autosoft: Replicate
(Unwired p123)