The checks at the airport are relatively quick. The federal police stands right outside the plan and does a quick visual check of your passport/ID. In case they need additional checks they will put the people aside in order not to block the debarkation.

On land borders it is a bit different. There are some delays because the traffic has to slow down which depending on the density of the traffic can cause a traffic jam. You might loose 30 to 45 minutes in a worst case (sunday afternoon during vacation season for example). Typical hot spots in Bavaria are the border on the A8 (Salzbug-Munich) , A93 (Kufstein-Rosenheim) and some larger Bundesstraßen.