So I came back from a huge hiatus and I noticed several of my pet's names have numbers in them now and it says something about legacy names. Does this mean that the rare names I worked for will forever have numbers in the name? Is there any way to fix this? Thanks for any help anyone can provide!

While you were on hiatus, your pets' names cleared for others to take and create for themselves. Now we don't have unique names anymore, so you should be able to restore their names properly to what they were before without numbers.

as said you can fix the name, but the Legacy Name will forever have numbers in it.

You can read about the new pet naming stuff here: FAQ about Legacy Names/Non-Unique Pet Names

If you don't like your pets having the legacy names with the numbers in them, you can clear the legacy names for free in the bathhouse.

https://subeta.net/explore/shengui_guo/bathhouse/cleanse.php

Note that if you choose to do this, it is permanent and irreversible, so proceed with caution and be absolutely sure you want to do it first.