I suspect that this is primarily an aesthetic question...but just in case there are some technical issues, I'd like a "show of hands" from you experienced installers regarding whether my wife and I--both DIY homeowners--should fill the nail holes and other imperfections in the reclaimed circa 1900 Southern Yellow Pine 2 1/4" strip flooring that we're re-installing in our remodeled master bedroom. We both appreciate seeing into the imperfections--makes them look more "natural" to us--so we're not keen on using an opaque wood filler--I've seen Timbermate ebony recommended on a couple of other posts to this forum--so I was thinking of using a clear polyester epoxy resin--also mentioned in another post...which seemed like a good idea to me until my wife raised the following question: After the epoxy resin cures will it be so much harder than the surrounding wood that it'll resist sanding to a point where each filled imperfection will remain "proud" of its surroundings?

If that's the case, we'd probably choose NOT fill the holes at all...but the reason we balk at doing that is because it seems obvious that open holes will quickly fill with dust, dirt and lint, which certainly isn't the look we're hoping for. So, if our choice is between: a) filling the holes with something clear; or b) not filling them at all, what's your recommendation...and why?

I think that filling the holes is important for a serviceable floor. Putty is the traditional filler which can be mixed to the color desired. Over time putty will harden and the floor is able to be sanded smooth. Are you going to sand the floor? Putty would be applied before the first coat of finish. Small holes are what putty is for.
If you have larger holes to fill putty would not work. You could use different diameters of dowels glued in place before sanding. This would keep the "look" of an antique floor. It takes a lot of time deciding which holes should be filled with dowels and doing the work. If you have water damaged flooring that has black stains in each nail hole I would use a different technique.
I prefer to mix some sanding dust from a fine sandpaper run on the floor edger mixed with 2 part epoxy to fill all the voids.

You will need to sand the floor to get it smooth, so putty would be the go to way to fill the floor after the first coat of finish has dried, if you miss little nail holes.
Epoxy does sand easily and if the floor stays dry the surface will stay smooth.
I add enough wood flour to make a putty that hardens so it sands flat without dropping into the grain or needing a "top-up" after the epoxy starts to soak into the holes. The epoxy filler will be darker than all but the darkest boards, unless you add color to darken it.

Holes must be filled and the floor must be sanded. This is important both aesthetically and practically.