At first I was annoyed by this, that being in a larger guild actually gives you in game perks, but then I realized... its a PvE game and who cares if someone else gets a bonus. As long as content does not assume you are using every single perk in existence (which is a possibility unfortunately).
The biggest consequence of this decision is that guilds may become even more internal focusing than they are now when it comes to groups. Having perks tends to get people used to others having them as well. Just one more reason to deny grouping with someone because their guild doesnt have <insert perk here>. Sorry, your dps is ~3% inferior due to not having the +2 damage so you would slow down our quest by <1 min... unacceptable!