yeah, a nuke uses relatively little matter, and is much faster to deploy and deny an enemy an area 
AND NGTM-1R is right, to make an IFF into the bugs can...and eventually would be... spoofed by a technology.
simply put, nukes pwn everything short of currently fictious energy sheilds , organic or not.
When did this get to be about nukes? At all? This was a comparison with
bullets. I am getting annoyed at people who don't read threads.
This IFF argument is kind of silly. Bullets don't have an IFF; that's up to whoever fires them. Same with whoever decides to deploy our hypothetical bugs at a target. Frankly I imagine our BioFoes aren't too bothered by the bugs or their actions; their end state (once they're in a 'secure area') might work as a xenoforming tool.
Interesting read. Yes, you are right that organism can synthesize complex molecules - but unless they can synthesize a gun or a nuke, technology wins hands down i nthe firepower department.
You are right - factories take time and resources to set up - but once up they can produce massive ammounts of hardware at a breakneck pace. Not to mention - DRONES. Slap a gun on a AI controlled mecha and you can send it into battle with no training required.
Factories produce at a linear pace from a centralized point with a big supply train. Our bugs here produce at an exponential rate, anywhere, foraging for their own supplies.
Drones require construction and programming, they can't make themselves. Plus, remember, these aren't meant to be compared with
drones. They're meant to be compared with
bullets.
One thing you're neglecting is that the "bugs" need biomass to grow. They need space. And they're pretty much constrained on one planet.\
Bullets need metal to be manufactured, plus a huge factory and the manpower to run it. And they're constrained to...well, wherever they're sitting, unless somebody picks them up and moves them.
Ammount of metals/ores on a planet >>>>> ammount of biomass. You can produce more bullets and guns than there are bugs in the universe. Bugs need to eat. Bugs need to grow. Nukes don't.
This is a comparison between bullets and bugs. Not nukes and bugs. If you make bullets out of an entire planet you'll have a lot of bullets, sure...but it'll take centuries. Millennia.
Also - nanomachines. Van Neumann probes.
Automated factories. Factories that build factories?
I already brought these up; thus my point about how the best technology will end up mimicking organic methods.