From the release notes of commies.oxp version 2.10:
2.10 April 2010
Corrected the role for the ecm-proof-missiles. Has always been wrong resulting in launching plain missiles for some of the ships.
I assume its this oxp giving the warning. It has been wrong there since before the release of Oolite 1.65. If you don't log errors, nobody will start complaining.
EDIT, no, not this oxp. This had the bug the other way round. It defined the missiles itself by their ship-key.
I think you need to narrow the search down a little. The Pods one for example (and quite probably the C&W one as well, and indeed some of the others too) is the awarding of a missile (for which EQ_MISSILE and EQ_HARDENED_MISSILE are correct as the award is by role not identifier key) rather than a like_ship reference.
That's also valid, as EQ_HARDENED_MISSILE is one of the role set for the ecm-proof-missile (have a look in the trunk shipdata.plist). In that case the line is saying that the default missile used by the ship is a hard-head.
Anything which uses the role of EQ_HARDENED_MISSILE is ok and valid, it's where the missile's idenfitier key is required but the "EQ_HARDENED_MISSILE" is used instead of "ecm-proof-missile" like you originally posted that would be wrong, for example like_ship.
OK I have more time and brain capacity to concentrate on this today.
First problem I caused was checking my oxp storage folder not addons and there are some older oxp's in there. I have now checked my current addons folder and there are only two oxp's with like_ship references to EQ_HARDENED_MISSILE.
Assassins shipdata.plist line 11is the only active oxp, the other one is in Realistic Shipyards Photon Torpedo.
It also seems I had placed a very old oxp in addons instead of updating to the new version which was the cause of most of the initial errors. I shall do penance by spending the day housekeeping my OOlite folders and polishing the rust on my Fer de Lance.