Another long-term effect of all types of refractive surgery is a loss of contrast sensitivity. This is not routinely measured during eye examinations, and the operational implications are not well determined, but everyone who has this surgery will lose 1 - 2 lines of acuity on low contrast testing. This would be a concern to me if a lot of my flying was done at night.
In military aircrew, there are a lot of advantages to not having to wear glasses or contacts (NVGs, NBC masks, etc), but the risk/benefit ratio might be different in civil pilots.