It very well could be a possible source of water infiltration. If you have plastic/neoprene plumbing flashings on top of your roof and you see daylight, it is likely where the neoprene has cracked or dry rotted. These flashings need to be replaced. Seeing light at HVAC/FURNACE penetrations is very likely as these typically contain a three part assembly that does not require an air tight seal to be leak free. An annual maintenance inspection would address these issues.