How to use RTC memory in NodeMCU to count awakes from deep sleep?
The simplest trick is to use more than one memory location. Have one, as you have now, as a counter, and then have one or more as a "This has been configured" flag.

Ideally you want the flag to have a very low probability of occurring randomly, so using a combination of a number of memory locations would improve that.

For instance, if you read memory locations 1-4 and look for four specific bytes, that gives you about a 1 in 4 billion possibility of it happening randomly.  

If you don't see those four bytes, you set the counter byte to 0 (or whatever you want your initial value to be) and set the other 4 memory locations to contain your 4 flag bytes. 

Using 8 bytes for your flag would give you in the order of 1 in 1.8x1019 chance of it occuring randomly.

These "flag byte combination" are often called "magic numbers" and are used all over the place to identify either what something is, or if something is valid.