Yes, I think they will be different and there are pros and cons for each:
1. Cooking then Freezing:a) Pros:- equipment is at right temperature to cook them all (oven can take an hour or more)
- subsequently quicker to serve with a meal (e.g. 1 min blitz, on high, in microwave)
b) Cons:- might be less crisp if using a microwave to reheat (an oven or grill is an alternative)
- takes more space in freezer
2. Freezing the Dough:a) Pros:- takes less space in freezer
- might result in a crisper naan
b) Cons:- takes longer (for dough to defrost)
- dough might be less manageable on defrosting (i.e. condensation or drying out)
- have to heat equipment up to cook (can take an hour or more)
- have to shape (takes more time and is messy)
I'm sure there are more pros and cons for each.
I prefer to cook them all and freeze the naans.
No doubt fresh is best (in this case).
Also check the replies to this here:
https://curry-recipes.co.uk/curry/index.php?topic=1448.msg21088#msg21088