Yes, the depth you cycle you battery to will have a pronounced effect on the number of cycles in it's lifespan. Most batteries have predictive lifespan graphs available from the supplier where you can predict the number of cycles your batteries will survive and, from experience, they're fairly accurate if you're using a good charger and perform very basic maintenance.

13.1 volts sounds a little high, usually fully charged is just under 13 volts and the 50% discharge voltage is around 12.1-12.2v. Gel batteries are usually a little higher voltage that lead acid though. Using voltage to check battery charge is prone to innacuracies if the battery has been under recent charging or load conditions and temperature can also have small effects on the reading. You should never discharge a deep cycle leadacid battery below 12v as a rule of thumb which will by 75% discharged at that point. Also try not to leave the batteries in a low state of charge for any length of time, obviously if you're only using solar or wind to recharge them it might be unaviodable but in that case select batteries accordingly.