Yes, let them know you are arriving late since WDW practices 'room ready'.
You check in (any time) and if there is a room ready, you get it. To me (don't blast me everyone), this has caused folks thinking they can check in in the early AM and get their vacations started and those of us who live far away or are unwilling to take an add'l day of vacation to arrive early, get the 'left overs'. With my ressies now, I let them know I'll be arriving late. Don't know if it helps or not, but makes me feel better!