which is more efficient? Replacing or recharging?

Solution 1:

Update 8/14/2017:

Things have changed yet again since the original answer and update -- several updates ago (as @Taz mentioned) the Seamoth can be outfitted with a Solar charger, so if you're close enough to the surface, and it's daylight, it will auto-recharge. (Note one way of recharging spent power cells without a power-cell-recharging unit in your base is to replace it with an empty/low power cell while near the surface.) That coupled with the recharging stations (again, that can be placed on a base, or even in your cyclops) makes recharging always a good move.

Update 8/27/2016:

Now that power cells are rechargable, This changes my answer slightly. Keep in mind that when you charge the Seamoth docked in the Cyclops, that it drains Cyclops power. With that in mind, however, you can now build a power cell recharging station on your Cyclops, and according to the wiki, gives a net-gain of energy for the cyclops. This means that recharging the power cell will use less energy then you get from a recharged one. I can see this getting fixed eventually, but for now it's by far the most efficient usage of power cells.

I keep 4 or 5 of them in my inventory for either excursions in the Seamoth, or to replenish the Cyclops ones, and when the Cyclops is at by main base, I just recharge the power cells in the base, which uses thermal and bioreactor energy. Since I have several exterior growbeds with creepvine growing, I have a virtually unlimited supply of biomass to use. (Not to mention an aquarium full of fish.)

It really depends on how much you move the Cyclops around, thus using more of it's energy. It's more efficient (resource-wise) to explore in the Seamoth, but once you get the power upgrade for the Cyclops (that's something you can get from the Aurora easily once it blows up) it seems like it's better to use the Cyclops to recharge the Seamoth's battery. That being said, when I go on a far-away recon mission in the Seamoth, I always pack an extra power cell for those times I don't have access to the required 1.21 Gigawatts needed for the return trip. :) Efficiency doesn't mean anything when you're stranded several kilometers away from your sub.

Solution 2:

If you need to use it immediately then replace it but if you have the time then it is better to let it charge.

Solution 3:

Not too sure why the option of a solar charger for the Seamoth hasn't been raised. Perhaps it may not have been in the game at time of the question.

The Seamoth Solar Charger gives 1% of energy every second. So in 100 seconds, you will have a full charge providing it is daylight. This may have a higher outlay but in the long run will be more efficient.

Source: Subnautica Wikia on the Seamoth Solar Charger