The only time animal checks took more than a few minutes was in Brazil (GRU) arriving late at night when the agent on duty didn't speak any language other than Portuguese and had to send for someone who did. You will not run into this issue at RTM.
Take the red lane ("things to declare") when going through customs. The officer inspecting your animals will likely give the documents a cursory glance, see that everything seems complete and in order and send you on your merry way.
To speed things up, don't bring (larger quantities of) meat-based pet food.
Rotterdam Airport is officially designated as port of entry for animals into the EU (click) and as such has staff on duty to inspect them in a timely matter.