Does pin hole in woofer affect sound quality?

No. From years of experience and having owned literally hundreds of speakers; NO. A pinhole does NOTHING to the sound of a speaker. Carry on enjoying your speakers without ever worrying about it again!

A pin hole will help cool the woofer, although a whistling sound may occur.

I suppose it would be too simple a thing to switch them and make judgment.  We can't have sensible solutions in HiFi.  :(

No! You do not want to use anything that dries hard! The edges of the patch might form a stress riser, a place where the cone might fail. 
Take the woofer out and apply some masking tape behind the perforation.
Tamp some black GE silicone into the hole leaving a slight bulge. Clean around the hole leaving a 5 mm patch. Denatured alcohol works great to lean up silicone. Let dry for 24 hours then remove the tape. Good as new.

Pin hole, not a problem, but:

sounds like you keep your grill cloth on, so cosmetics not a problem. Got a wife, girlfriend, mother? A little nail polish will do it, comes with the tool you need. Like spray paint, a few thin coats not too thick to start. Lay it on it's back so it doesn't drip down the face of the cone while drying.

AGE deterioration? is paper cone still stiff? Is surround good and still springy, strong enough to keep the woofer centered properly? Voice coils can rub on the magnet if not centered.

I have re-coned my woofers from 1958 twice, I am about to check them soon. My old ones are paper cone's with cloth surround. I paid a pro do do it the first time, did it myself the second time.

Kits are available to restore most speakers, far less costly than replacing the woofer. Check on eBay, online, is OEM around?

I would replace them both so they have equal strength to the air.

I also replaced the surround of my vintage SUB, newer foam surround had rotted.