How many wallet.dat files can you manage at the same time?
As many as you want.
What is the difference between using the native segwit format (that begins with b) from the one that begins with 3?
Is it just a temporal way to use segwit until the ones that begin with b are available or there are any pros and cons?
Native segwit addresses (bech32) make native segwit outputs which are smaller than the P2SH nested ones (3.. addresses). This saves you 22 bytes when you go to spend the output.