"- Is it possible at all to take the deformation of the shot peening into account when machining such tight tolerances?"

This is done all the time when parts are sent to us for shot peen. You need to determine which process is changing the hole size( peening or cleaning), not always but most of the time peened holes get smaller not larger. Is it possible the holes could be being peened well beyond 100% coverage? If so, this would likely be the cause.

I would suggest manufacturing one part and measuring it to sure its within tolerance:

1) Then send it to the shot peen source for peening. However, DO NOT perform acid cleaning yet.
2) Once peening is complete remeasure the part.
3) If the part is within tolerance return the part for acid cleaning then measure again.
4) If the part is NOT within tolerance after peening then adjust your pre-peen dimension accordingly to factor in the changes caused by peening.
5) Manufacture another part with the new pre-peen dimensions then repeat the steps above.

Hope that helps,

Walter A. Beach
Vice President
Hydro Honing Laboratories, Inc.
d/b/a Peening Technologies of Connecticut
8 Eastern Park Road
East Hartford, CT 06108

860-969-6207