Yes. The loot penalty isn't as severe as it used to be, but there is still a penalty in place. Sometimes attacking down is unavoidable if your alliance has more powerful bases. However, if you have your lowest level cc's hit your opponents lowest level cc's and you already have 3 stars per base, have everyone attack up with their 2nd attack if they are confident enough in their attacking abilities. We would hit opponents 30-40 levels above us to make up for the loot penalty for attacking down.