I don't know for sure, but it is logical to assume that repeated high current draw (from the thruster) would decrease the battery's life expectancy. It generates a lot of heat and heat typically breaks things down faster at both the mechanical and chemical level in the battery.
What I can say for certain is the OEM Universal Batteries that come with the boat have a less-than-stellar record. There are numerous posts on the forum about the premature death of these batteries, some in less than 2 years. I got 4 years on my R31 before they died. My recommendation is to replace all your batteries soon, as I suspect they will all fail in short order, even if you are only seeing an issue on your thruster right now.