Then again, the transporter already fills many of the practical/dramatic roles of the boat, leaving the shuttles somewhat high and dry.
Are they just bigger boats? A transporter can leave you stranded, but you can't be left stranded aboard a transporter, so the shuttles are needed to play that part of the boat role.
Shuttles can also do meaningful reconnaissance even when the era features the concept of remote sensors. They are the equivalent of shipboard spotter aircraft, then (fixed-wing or rotary-wing), bringing an extra dimension to recce even when the mothership already has "radar".
There's a little bit of everything in the mix when Trek tries to make a "naval" impression: auxiliary spacecraft and spacesuits may evoke the concept of diving, too.
No matter what the analogy, the most important thing is that shuttles are clumsy and awkward, plot-complicating elements. They don't facilitate, except through hindering. Thanks to shuttles, there can be delays, preparation times, detours, rendezvouses and problems with recovery that the transporter cannot provide. In that sense, equating shuttlecraft ops with something that is complicated in the nautical world is a fruitful approach: in the era of sailing, it would be the lowering of boats, but it could also be well decks, helicopter decks or flight decks - as long as these remain time-consuming, preferably man-in-the-loop types of operation. Having a "shuttle chief" is almost automatically desirable, even if his or her function is simply to be late, careless or powerless!
Timo Saloniemi