The thing to remember is that the Clans aren't stupid. They're very weird, and sometimes they do very stupid things, but they're not STUPID. The Omnimech is the pinnacle of a Clan warrior's possible equipment in-general, but they acknowledge the need for other, lesser units- thus standard Battlemechs, combat vehicles, even artillery (ewwwww). They may not LIKE using it, and it may be a stain on one's honor to be the one using it, but it still exists- because it has to. Not all situations call for an Omnimech solution, and there aren't enough of them to cover every job anyway.
Another thing to remember is that TROs tend to be comprehensive when it comes to Mechs and such, but it's not hard to imagine that there's a lot of solutions to problems that haven't made it to a TRO over the years- whether it's a one-off refit of a Mech on some backwater world, a specific upgrade to an assault tank to turn a particular one into a command vehicle, a few fighters modified by a merc unit to reduce ammo dependancy, a small production run of a light tank for a local militia... or a Clan naval unit.
So what would they look like, these 'unseen' naval craft? Would the Clans commit resources to refitting a Mauna Kea that came along on the Exodus? Would they produce new ones if they needed? Design something entirely new? (Not all worlds' oceans and seas are the same, so it stands to reason you'd build based on the conditions at-hand rather than commit to a cookie cutter approach). Maybe something larger, a Clan equivalent to the Jordmungand or something along those lines? (Again, if your world needs a hefty solution to waterborne problems...)
I know the 'if it works for your game...' answer sometimes rankles people, but it's true- if you want the Jade Falcons to have an aircraft carrier, go nuts and raise a green bird flag up the mast. :thumbsup: