How to implement a zoned low-voltage lighting?

Since it is low voltage, you could do things that are not OK with mains voltage, such as running 2 2-wire cables you can easily source (wire-tied together) where you can't easily source 3-wire cable. You could also use 3-wire UF-B as overqualified low-voltage cable. It might confuse the next person to see it, but it would be perfectly safe/adequate.

Wet-location switch boxes that are set up to operate a "normal" switch protected inside the box exist, and AC/DC rated switches also exist, though they are harder to find than AC-Only switches. I have not throughly investigated sources for wet-location low-voltage DC-only 3-ways at this point. Boating suppliers might be a good place to look, for instance.

If going with the 120V approach, I'll always suggest conduit as superior to UF cable.

I'd use relays for this

The simplest way to get out of this jam without throwing a bunch of lighting transformers at it would be to use single-pole/single-throw switches to switch on and off SPDT relays that control the lighting loads, as SPDT relay contacts can be wired in the same fashion as 3-way switches. For the switches, you can use Leviton 56021s with Bell 5123 (single) and 5127 (double) weatherproof covers; you have a couple options for relays, though. If you have space around where you're installing the switches, you can thread Functional Devices RIBU1C-N4 relays into hubs on the switch boxes; an alternative approach would be to use AP&C PAM-4 relays mounted inside the boxes, but this requires a fair bit of box real estate at each switch location. Both of these relays are rated for switching significant resistive load at 28VDC (7A for the PAM-4, 10A for the RIBU1C-N4), so 3A of LED lighting shouldn't be a significant challenge.