Just a cursory search on Oregon.edu's online dictionary has produced a number of words related to ships and boats like steering with a rudder, the rib of a ship, and the sail of a boat. The root word, acalli which can mean canoe as well as ship and boat, seems to have been used to make all sorts of words related to ships rather than using the loan word navío taken from nave.
I'm wondering how many people may have had experience with ships enough to have these words enter the lexicon to such a degree for Molina to include them in his dictionary.
For those wondering, I've included the list below.
acalacana - to calm the boat or ship
acalco - relating to boats; in a boat; in the boat
acalcuexcochtli - stern of a boat or ship
acalhuelteca - to steer the ship with the rudder
acalhueltecac - he who steers the ship with the rudder
acalhueltecani - he who governs or guides the ship using the rudder
acalhuelteconi - the rudder or other steering device on a ship or boat
acalhuia - to send something in a boat or ship; to go about in a boat or ship for recreation
acaliyayaliztli - the well of a boat or ship
acalla yayaliztli - the lower cavity of a ship, where water penetrates and accumulates; the bilge
acallancoani - cargo or passage on a boat or ship
acallanehuani - a shipment or passage on a ship
acallanehui - a person who ships things
acallanehuia - to transport by ship
acallanpanaliztli - shipwreck, where the boat breaks up
acallapanaliztli - a shipwreck; where the ship breaks up on the rocks
acallapani - to experience a shipwreck, with the boat breaking up
acallaxtlahuilli - load, cargo, freight on as ship
acallaxtlahuiloni - a shipment, freight on a boat
acalli cemmantihuitz - fleet of ships
acalli - ship, boat, canoe, etc
acalmaitl - the rib of a ship
acalmiatl - the flank of a ship
acalnemachiliani - he who steers the ship
acalquachpanitl - the sail of a boat or ship
acaltema - to put a cargo on a ship, or launch a ship and put something in it
acaltetl tlatilincateconi - ballast of a boat or ship
acalyacatl - the prow of a boat or ship
atlan nontlatoxahua - to lighten a ship’s load in the storm
atlan tepehua - to unload or to lighten a ship
atlan tlaza - to unload or to lighten a boat or ship
atlantoxahua - to unload or to lighten a ship or boat
metzhuehueloa - to dislocate one’s ship
nopan tlapani in acalli - to get in a shipwreck
toxahua - to unload or lighten a ship
I'm curious why you believe that these words required the presence of large (ocean-going?) ships? It seems to me that most if not all could just as easily be used in the description of small boat traffic on lakes and rivers as well.
Aside from what /u/DoorToSummer said, I would be careful about interpreting these words from an Anglophone perspective. the Nahuatl languages are highly agglutinative and polysynthetic, which means that where in English we might say:
"I shall make somebody give something to you"
In classic Nahuatl you would use simply one word. A single heavily inflected verb:
"nimitsteːtlamakiːltiːs"
Broken up as follows:
/ni-mits-teː-tla-makiː-ltiː-s/
I-you-someone-something-give-CAUSATIVE-FUTURE
Therefore a lot of these words you list are in fact just the natural agglutinative process in languages like Nahuatl in which existing words are combined and inflected to form new words.