Sheldon (EDH Rules Committee) has answered this question directly.
The RC has discussed it and for the time being thinks that multiple Rats is OK. We reserve the right to change our minds down the road.
Although some rules differ from the official MtG rules (i.e. "outside the game" ,Living Wish, is handled differently than other casual formats), Relentless Rats' ability is covered in CR 112.6m. If Relentless Rats were banned in EDH, you couldn't use any copies, but since it isn't you may use any amount from 0-99 copies because [CR 112.6m] specifically allows you to ignore [CR 903.5b].
112.6m An ability that modifies the rules for deck construction functions before the game begins. Such an ability modifies not just the Comprehensive Rules, but also the Magic: The Gathering Tournament Rules and any other documents that set the deck construction rules for a specific Constructed format. However, such an ability can’t affect the format legality of a card, including whether it’s banned or restricted.
903.1. In the Commander variant, each deck is led by a legendary creature designated as that deck’s commander. The Commander variant was created and popularized by fans; an independent rules committee maintains additional resources at http://mtgcommander.net. The Commander variant uses all the normal rules for a Magic game, with the following additions.
903.5b Other than basic lands, each card in a Commander deck must have a different English name.