We filled open knot holes with G5 epoxy by West System. It is a 2-part epoxy that we mixed in small batches (4 oz. plastic cups) and dabbed it in the holes before sanding/finishing. It hardens fairly quickly to a hard, light amber-colored material that blends well with antique flooring.

We recently installed some reclaimed heart pine. There were some bolt holes, like 3/4" diameter, in addition to smaller holes. We either culled out the worst holes or patched them with wood plugs or dutchmen. It was okay because the original flooring had been taken up, re-milled, and had scads of nail holes and other damage from removal. The new flooring (with bolt holes, supposedly from large timbers used in warehouses or factories) supplemented the original stuff to make up the shortfall, which was almost 180 square feet. The floors ended up with tons of character, and look truly at home in the 1817 rooms.
Your outcome depends on the skill of your carpenter.The repairs can be effected on the workbench before the material is installed, as sometimes that is the more efficient method. Dutchmen (rectangular patches) can be accomplished by routing out a recess, which need not be the full thickness of the board; 3/8 is fine. The router is guided by wooden straightedges, and the dutchmen is cut to the exact length and hand-planed in width until it fits perfectly. If the grain is chosen properly, it can blend in very nicely.
Wood repairs only, not epoxy please.
Casey

Wood repairs only, not epoxy please.

We had hundreds of spots to fill, making a teeny wooden patch for each one was completely impractical. Most of the spots we filled you would never know that they weren't always black knots instead of holes. I like the character grade look, YMMV

I'm just sayin' for "bolt holes", no gross epoxy. Any tinted hole filler is great for nail holes. I like Abatron epoxy, it can be tinted with aniline dyes.
Casey

Fourkidz-- We have reclaimed heart pine which has the bolt holes but didn't fill them because they are a part of the character of the floor. Just want to worn you about wearing high heels on this type of floor. The damage will be horrible and I wouldn't want anyone wearing them on heart pine. It is incredibly soft as you probably know. You will love the look of this wood.

Hi,
This is the floor I refernced above, it's 90% original floors from the house supplemented with new reclaimed. The original stuff has more character from the old nail holes and powder post beetle tunnels.

The hallway floor is more than half new; all of it from the side doors to the foreground is new. The first six feet in from the front door are original. It blends really well.
The finish is a custom blend of stains, two coats, and three coats of colored waxes.
Casey

Beautiful floors, nice work.