Originally Posted by
Xanthorrhoeas
If I had to take a punt at the timber I would say that it looks like Elm to me, or at least the top does. The sides are a ring-porous timber by the look of it, but not any figure that I have seen in Elm. But then, the most Elm I have seen is in seat furniture.
Many of the early antique tables that I have seen had the top fixed to the frame using glue blocks only. That is, no buttons or screws/nails except those added later. Because the glue blocks were attached with hide glue and that couldn't take the stresses they often fell off. I have had to re-glue the blocks on my earliest table about 4 times in the last 30 years. If that was how your table top was attached there should be witness marks of the remains of the hide glue in rectangular patches inside the top of the rail and on the underside of the table. They may be pretty faint.
I would defer to others with more experience of nails than I have (like auscab) but those nails look to be similar to nails that I think were used about 1900-1920's in Australia. They would have been added in later as the top became loose. It is rare to find a utilitarian table that doesn't have later screws or nails bashed through the top and I even have a very fine cedar extension table that has some screw holes.
I would recommend that you stay away from tinted beeswax as a filler. It is too soft. There are hard wax crayons that you can buy in a range of colours from brands like Liberon that are better. However, the best solution I find is to melt button shellac into the holes with a cheap spade bit soldering iron. It is very hard and fully compatible with your finish. I have bought buttons from Shines Shellac in the past. I can look up their number if you are interested (PM me).