If you're storing only the hash itself as base64, this shouldn't materially alter the one-way nature of the hash or its protection of the original plaintext.
As long as no other pre-hashing plaintext data or related metadata is included (that would in any way hint at potential plaintext), then a leak of base64-encoded hashes wouldn't be any easier to attack than a leak of the original hashes.
An attacker would simply analyze the data, discover that it consists of base64 strings, convert them back to their original hashes form, and then carry out the attack. This won't slow most attackers down, but it also won't make things any easier for them.