Hand-counting RCV is no big deal, especially if you have enough tellers.
I have seen NOTA within RCV be handled a few different ways.
1. NOTA can be eliminated (candidate NOTA). On-par with all of the candidates. We just did this.
2. NOTA cannot be eliminated, and is an option (optional NOTA). This is the method I prefer, personally. A voter has the CHOICE to write NOTA or not. By choosing not to, they are saying "I don't care who gets elected, if the ones I want are eliminated" if their ballot becomes exhausted. By choosing to use NOTA, the voter specifically says "I do NOT want anyone except those on my ballot" and therefore the ballot never be exhausted. RCV requires a majority of unexhausted ballots to win, so this voter choice matters.
3. NOTA cannot be eliminated, and is the last option on every ballot (mandatory NOTA). A voter has NOTA inserted at the end of their ballot no matter what. This increases the chance that NOTA will win, but also ensures a non-NOTA option must win a majority winner of all ballots cast because no ballot is ever exhausted.
As noted, I personally prefer #2 (optional NOTA) as it provides maximum flexibility to a voter.
ken