Does pin hole in woofer affect sound quality?

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.

If you find a pin of the same diameter, you can put another 'mirror image' hole in the other speaker for balance.

Seriously, if it's a paper type cone, you can sand some wood, mix the sawdust with a little wood glue to create a filler paste. Then patch carefully. If need sand lightly and use a dark grey, black or suitably colored marker to blend in the color.

I would practice filling in pin holes in card stock to determine how much glue/dust ratio works best.

Although it sounds like a lot of fuss, if the cone is very smooth, then you don't want to add texture...so best to do as little as possible...you want to have the least amount of effect on resonance/mass/performance.

As mentioned, best to remove the speaker, apply a low stick tape to the back (scotch 811) of the cone, fill the front, lightly smooth/sand (only if needed).

Conversely, you can tape the front and fill the back if the woofer basket allows access. That might look cleaner.

Thank you everyone for your responses. I did repair the pin hole with a dab of black silicone and wiped it smooth with the diaphragm surface. The paper cones on the woofers still appear to be stiff and the surrounds still appear to be springy and strong enough. One tweeter no longer worked, so both tweeters in both speakers were replaced with the Peerless by Tymphany tweeters recommended to replace the originals. The oak tops have been re-glued to the cabinets and new grill foam has been ordered to replace the worn and saggy original covers. That should complete the restoration of the Time Windows. I plan to test them this afternoon and if I can figure out how to upload a photo to the blog, I will do so.