Q:

Are Exterminatus weapons ever used against ships? 

It seems like if a cyclonic torpedo can destroy a planet, it could also destroy any ship.   Same idea with virus bombs.   If the virus from a virus bomb can wipe out all life on a planet in short order, it seems like it could also do that to a ship.   Getting it on the target is simple; load a boarding pod with a virus bomb instead of marines. 
So do they do this kind of thing, or no?   If not, why not? 

A:

Wildly Inefficient
The only instance I can think of is when HDMS Lord Solar Macharius uses cyclonic torpedoes (of which they only have a few, specially issued for the task) to destroy a particularly nasty ork infestation in an asteroid belt.   They're fired at the ork Roks (basically asteroids with engines/guns) to great effect.   I'd point out though that at the point in the Gothic war where this happens Battlefleet Gothic is on the ropes and desperate to clear its supply lines, and everyone involved acknowledges that while effective it's a desperation move. 
The Imperium's technology is vast, but their production methods are archaic.   The more impressive the technology, the more complex the production.   That's not just the actual science behind making a plasma gun or whatever, it's the mysticism surrounding it.   This is a culture that requires a trained cult to do things like press the 'On" button for fire-fighting equipment (Battlefleet Gothic main rulebook).   The creation of Exterminatus-grade weaponry is a closely guarded secret by those few tech-priests which posses the knowledge to manufacture them.  They take AGES to produce (BFG sources indicate a single NORMAL Imperial torpedo takes a decade to manufacture) and are exceedingly rare.   To the point where an Inquisitor Lord with all their power and trappings might have access to a single cyclonic torpedo or virus bomb, but probably not both at once.   Likewise Imperial Navy Battlefleets and Space Marine Chapters might own a handful of such weapons with resupply being hard or even impossible for some makes. ( for example, if it's Phosphex based they don't make those anymore.) 
So we're talking about weapons that may be centuries old, and may or may not be replaceable.   They're designed primarily for a single function, to destroy a planet.   Using such a weapon against a ship would probably be seen as a criminal waste of resources at best, and tech-heresy at worst. 
Now there are things I would classify as sub-exterminatus that could do the trick.   Massed Nova cannons or Bombardment cannon fire could purge a world.   Heck, battleships are frequently described as heaving broadsides that could "wreck continents" and their primary mission is blowing up other ships.   But the one-shot=planetkill type weapons aren't something an admiral wanting to keep his position (to say nothing of his head) would use without some overriding need or specific order.