I would recommend explicit checksumming in data backup scenario. Main advantage is that this way your data is "multi-modal" (in shipping industry lingo). I.e. you can move your data between different computers, different filesystems and all the checksums move along. So when it's time to move your data to a newer disk you just copy it and you're not tied up with the choice of file system you made before. Scrubbing is easy too.
Plus you will not lose any files without noticing the fact - even when file is deleted it's still in your md5 file.
And you don't even need any scripts to handle your data - all decent filemanagers (e.g. "Total Commander" / "Double Commander" etc.) can do md5/sha/whatever on selected files on the click of a button.