An update came out yesterday and nixpkgs still shows the previous one. Should I wait one to a few days or go ahead and install the flake version of the software?
An update to what?
You can check on Pull requests · NixOS/nixpkgs · GitHub if there’s a pull request for it, or in GitHub · Where software is built if someone has requested it.
If a pull request was merged, you can use https://nixpkgs-tracker.ocfox.me/ to see to which channels the update has arrived.