they are a remnant of times where every byte saved counted - instead of the patch distributing a full updated mis file, it only applied the (smaller) dif file, which loaded the fixes/changes on top of the original mis file already present in the game install.
this is very annoying nowadays because the dif files, if present, can wreak havoc if you intend to/are using properly updated/patched missions (TFix).
if you are asking whether you should use difs in your patch, the answer would be no - get the unstripped T1 mission package which should have all the vanilla fixes and use that.