Im a 40 y/o male married for 16 years and was just diagnosed with 2 small genital warts on my penis. both my spouse and i are certain we have been faithful. why are they showing up now, and how did i get them?

Two small warts could be just garden variety warts. If they are HPV, you were probably infected many years ago and the virus reactivated recently. HPV lesions are very small, 1 to 2 mm warts, and generally occur in clusters. See your doctor and have them removed.

Appearance of genital warts depends on many things like aggressiveness of the type of virus, your body's immune system etc. So there is a possibility you had the infection before marriage which just manifested.