It is not good news, but to be truthful, it is iffy as to whether or not a home inspector will be able to reliably detect subtle seepage around skylights. Many factors and variables are involved and sometimes you can, sometimes you cannot.
Flashings and seals around the glazing at corners of skylights are vulnerable to leaks. The watertightness of any given skylight is dependent on the quality of the skylight itself (manufacturers’ responsibility) and proper installation of flashings-seals and the placement of underlayments at the top side (responsibility of in-the-field installers).
Velux manufacturer specifications, various means of waterproofing
Once the roof surface is in place, shingles or other roofing materials obstruct the view of the flashings and underlayments.
Roofing materials obstruct the view of flashings and roof felts
Usually, even when attic access is possible, the view will be restricted. The light shaft, at a properly installed skylight, will be fully wrapped with thick insulation. The photo below, for illustrative purposes, is an example of a skylight that is partially wrapped.
Attic photo, insulation is wrapped around light shafts
Sometimes seepage, moisture intrusion or damage might be detected at the bottom side of a skylight when looking up from inside a building.
Obvious water intrusion below skylight
Unfortunately, to complicate matters, some degree of staining below a skylight does not necessarily mean that the skylight is leaking. Stains are frequently caused by drips as warm interior air rises and condenses on the cool surface of the skylight glazing.
Since skylights can be problematic, watertightness reliant on a number of concealed components, any homeowner should closely monitor skylights. On a regular basis, clean moss and roof debris from around skylights.
Qualified roofer to clean around skylights
Monitor skylights from interior space and, if any indications of seepage become apparent, promptly contact a roofing contractor. Identifying leaks, sooner rather than later, reduces the odds of, at a later date, requiring costly repairs.