Nerve poisons/Viral infection? Perfect to take out the crew on a space ship.
The matter comes down to getting it INSIDE - space ships don't exactly have screen doors

Such vessels are, like warships, segmented and can be sealed off in case of a hull breach. Simply close off the infected area, and if it comes down to it, jettison the atmosphere into hard vacuum.
Radiation? Same goes here, plus an atomic explosion near a space ship would inevitably destroy almost all electrical components on the ship, EMP hardened or not.
Heavy metals are infinitely more effective against combating radioactivity than organics. Even neutron radiation would be significantly slowed passing through a hull than a carapace. Given the intense radioactivity in space and the fact that so far, no astronaut has had three-headed children, I think it's safe to say that even the relatively thin skin of an unarmored Apollo moon lander is pretty durable against radiation.
As for EMP, well, I can't say exactly, but I doubt you can either. What I DO know about EMP is that, like ANY electrical signal, it's really little more than extreme induced interference. Triaxial cables are double-shielded and both shields serve to ground out the extreme voltages an EMP field induces in conductors, leaving very little to penetrate to the core. In fact, even F-15s, with what I can say personally are relatively fragile avionics packages, are nuclear-capable and can survive the EMP - it's not a stretch to say in the future that shielding methods will get better - a superconducting shield around fragile computers would likely be the most effective, if not COST effective, method of protection. I won't say for certain, however, and sure, EMP could be considered - but I'd rather hedge my bets on something technology from 1970 can protect against, rather than something nothing can protect against (radiation poisoning).
Micrometeoric impacts? Same goes here.
What? You're saying you think a micrometeor could punch through a hull just as easy as it could through a carapace? Remember that I also mentioned two things - 1) The fragility of internal organs and vital fuctions, and 2) The ease of redundant systems, as well as compartmentalized breach sealing on a mechanical ship. This is a non-point at any rate, because if you threw enough money at a ship, you could design a super-sensitive radar to track and shoot down incoming micrometeorites. I'd love to see any form of organic critter with that ability.
And you could attack a non organic ship successfully with computer viruses.
Perhaps, but once again, it's a factor of penetration. The F-15 was made in the 1970s, and has a HEAP of cryptological countermeasures, ECM, ECCM, and backups in case of security integrity issues. Breaking such keys, which are changed once a day, would not only be nearly impossible, but it'd be far more beneficial to keep the link alive and monitor enemy tactical situation updates than it would be to attack and have the system closed down on you. To say that a Quantum Supercomputer or whatever running these ships would have nearly unbreakable cryptological systems is something of an understatement. You don't just float over to the hull and plug in your USB virus.