In Metroid Prime 2: Echoes, a particular enemy can hack Samus's Suit. It renders Samus's visors and battle computer inoperable. To counter it's effects, Samus must reboot her entire system. In multiplayer, Hunters can hack each other's suits if they get an upgrade for it.
Breaking into Samus's suit would probably be a very quick job, I agree with dark1365. However, if Samus reboots, she will be fine. Samus may also be able to hack into Cortana, in Metroid Prime 1 the Space Pirates complain that the security on their computers was easily being hacked by Samus. So the hacking war goes both ways. Now we have Cortana vs. Samus Aran.