I am an experienced master carpenter and construction foreman. I have overseen many floor restorations. The guys I used ALWAYS filled all of the cracks and holes. Most of the time they mixed some of the native sawdust (I am assuming that you sanded the entire floor with professional grade sanders) and mix it with this special stuff that the floor guys use. They only use the fine dust and mix it into a paste with this clear brown glueish stuff. You can probably get a can from a local flooring guy or find out where they get their supplies. I have seen guys use the same polyeurathane that they are going to use in the finish as the glue for the dust. I have also seen tinted drywall compound used as a filler in new oak applications (believe it or not, it works great). Usually the filler is trowelled over the entire floor. Then you final sand. below some comments from another industry website.
Generally, filling of nail holes, blemishes, cracks, etc., should be done before the fine sanding cut. Use a commercially prepared wood flooring filler. Some fillers may need coloring or may not take a bleaching operation; check with the supplier or manufacturer. Also, it may be necessary to trowel fill the entire floor, particularly an old floor, due to the extent of cracks between strips. Multiple character marks found in #1 and #2 COMMON Grades which are fillable grades may also require trowel filling. Trowel filling should be done before the medium or final sanding cuts. Let the filler dry thoroughly before proceeding with the sanding. (Overnight is best.) From: http://www.nofma.org/installation.htm