Many men have small bumps on the underside of the head of the penis. These are not warts. Most warts occur further down the shaft.
Yes, it is possible for warts to lie dormant for years. However, what you have does not sound like a wart. Also, you've been with your wife for years, and if she does for regular Gyn care--and she obviously does--then the doctor would have noticed if she had warts, and she obviously doesn't.
If the bump comes back, show it to a dermatologist, just for reassurance.
Congratulations on your new child!
Dr. Rockoff
PS
I know you will probably not approve but I did attempt a self diagnosis via the white vinegar, several times. There was no change to the vesicle(postule, papule, nodule?). All it did was irritate my genitals. Thanks again.