typically the aerospace industry peens holes using the same technique, quadrant peening.

by positioning the nozzle at 45 degrees and peening the hole from 4 quadrant positions (0, 90, 180, 270 degress) , both sides of hole.

if the hole is L/D less than 1, this enables line of site and eliminates the need to rotary lance peen the hole - and having to used masked strips.

To represent the hole, you can lay the almen strip flat over the hole , not along the hole axis, since you are peening at approx. 45 deg.