Question: As a rule of thumb, how often should seals be replaced on roof-mounted features/accessories (Skylights, air conditioner, antenna, etc.)?
Answer: You should always follow your manufacturers recommendation on inspecting and refreshing your seals. The owners manual should also recommend specific sealants that are compatible with your specific roofing materials.
For instance I have a fiberglass roof and my manufacturer recommends inspecting all penetrations on a yearly basis and resealing where needed. I have had to replace the caulking around a skylight and around the satellite antenna when I had to replace them.
I do a thorough inspection and reseal upper (roof) and lower belt lines, around all marker lights, windows and the refrigerator vent on a yearly basis. I replace caulking when it stops looking smooth, I see visible cracks/voids or when I suspect a leak.
If you are concerned about the seal under the air conditioner then I would suggest looking at your air conditioner owners manual and torque down the seal to the correct specification. If the seal is at its correct torque and it still leaks then you will have to replace the seal.