You had condom protected everything. I wouldn't worry about this.
There is a very low risk for syphilis, hpv and herpes, but it's low enough that I wouldn't spend any time worrying about it.
Holes in condoms are a myth. If a condom fails, it is catastrophic. You'd know it. You don't need to test it with water.
Nothing will change this answer, even all the "what if" scenarios your brain will create.