In the TNG SA novel “The Haunted Starship” the Daedalus class ship ‘Benjamin Franklin’ NCC-013, is still in service in 2354, nearly 200 years after its launch in 2179—however while it is still in service it has been retired from active service and serves as an Academy training vessel. (http://memory-beta.wikia.com/wiki/USS_Benjamin_Franklin_(NCC-013))
Couldn't they have just bombarded it with enough short lived radiation to sterilize the ship completely? They probably didn't do that with the Landtree because Worf wanted some live fire target practice.
I think just leaving all of the airlocks open for a few days should completely wipe out any life forms, unless they can live through hard vacuum.
They can also irradiate the ship with something like they used in 'Starship Mine' that will kill anything organic.
That might work for some. I remember an episode (of Next gen, I think? Not sure) where someone suggests that the virus/organism could just be left in the vacuum of space but then someone says that it would just go inert and if it comes into contact with other lifeforms could reactivate and kill everyone.
Well, even asteroids contain a lot of raw materials, as will many uninhabitable planets (which are likely very common). Also, don't forget replicator technology in Trek means that a lot of stuff can probably be made from other less useful matter, at least in the TNG era.
Probably a certain number would be kept in reserve-fleet status. Mothballed but ready to be put to active duty rapidly. This would not be the same as a breakers or salvage yard. You might want to focus on ships that are uniform and easy to keep upgraded, which might explain every time whatever equivalent to DEFCON Starfleet has changed for the worse, Federation space is curiously bristling with Mirandas and Excelsiors. Less common ships like Connies and Crossfields would be a pain to keep maintained