There is manual NUCing which is what is required by your OTS and by Trijicon scopes were you do everything. There is automatic where the scope does everything. There is semi-automatic where you press a button or buttons to initiate the NUC sequence.
The issue isn't covering the lens, but covering the sensor. You probably hear a little 'zzit-zzit' sound when it NUCs. That is the small cover moving over the sensor and then off again.
By the way, you would probably do good to set your Pulsar to NUC in 'semi-automatic' mode. That way, you determine when you want it to NUC. It will save you a bit on batteries and keep it from NUCing in the middle of some critical time such as when you are trying to take follow-up shots or just as a count-down (group hunt) reaches "1" and you are all supposed to be shooting.