This is an interesting problem and provides plenty of opportunities for Murphy to mess with success. As an ocean engineer in an earlier career, you need to be positively paranoid about humidity and condensation throughout your system. Use a waterpoof enclosure and if there are any openings, even for a cable through a grommet/fitting, make sure they face _down_ to facilitate draining any condensation that might form. Put in as much dessicant as possible to soak up humidity and prevent condensation (like those little bags of resin that fall out of many product packages). Surround the enclosure with as thick a layer of foam or fiberglass insulation as possible to minimize temperature swings (especially downward when condensation forms) - of course, you also need to leave a hole for the camera and place the lighting where it makes sense. Also become very close friends with silicone sealant, lots of it.
As for batteries, lead-acid, advanced glass mat (AGM), and gel-cell batteries all must not be discharged beyond certain levels (60 ~ 70% for lead-acid, 40 ~ 50% for AGM/gel, depending on specific model) or permanent reduced ability or inability to recharge will occur. NiCd, NiMH, and LiPolymer can all be fully discharged and, in fact, should be, especially NiCd to minimize the "memory" effect (which also occurs in NiMH batteries to a lesser degree).
As for the parts of the system that perform the actual task at hand (what did we come in here for? ), taking photos, I would tend to go for Keep It Simple, Stupid. All you really need is a camera and a timer, period. Trying to depend on a Linux-based system on hardware that has no track record that has to boot up and power down without fail daily for many months, while it sounds good in theory, is a recipe for disaster. Yes, the components have each been used separately in other systems, but, this particular combination is barely in production (who knows when you can buy one, much less a backup?), the OS is still a work in progress, and it will remain so for months to come. Integration of successful components increases the odds of creating a successful system, but, it is far from a guarantee of success.
There are plenty of options and the first one Google listed is the TimelapseCam 8.0 at https://www.Wingscapes.com/timelapsecam
for $109 (free shipping), which can use SD cards or downloads via USB, and lasts at least a month with 4 AA batteries. The specs suggest battery life of months with longer intervals between photos, which range from every 10 seconds to once every 24 hours. I"m guessing an auxiliary battery pack can be wired in for longer periods, even if a power jack isn"t built in. There are probably less expensive options, but, this is weatherproof, is equipped with a threaded tripod-style mount, etc. You"re going to need to spend close to this amount for a Pi, camera, case, batteries, etc., plus shipping, manhandling, etc.
I"d be interested to hear what you decide to use and how it turns out.