I've seen a dozen such rankings, each of them with different figures, depending on which type of races are included.
The problem is: criteriums are and always have been fixed in advance by the organisers but kermesses are not in theory at least. I have many accounts of the facts that kermesses were true competitions and fiercely fought for races (the few that remain still are true competition, to my knowledge, like Gullegem Koerse), even if they are not official races and in practice there was a lot of fixing on the circuit, just like in official races, for that matter. So you gotta be pretty elitist to discount kermesses in such classifications. Besides, Merckx was not a kermess regular, least of all club race regular, but perhaps at the start of his career.
He went to the track, for the money.
The problem is that on a palmares, it requires a great deal of attention to separate what is a criterium to what is a kermess. I'm not knowledgeable to do that.
No, contests within Sixes have never come up in any palmares whatsoever. However according to Achiel van den Broeck in "De miljoenenfiets van Van Steenbergen" (De Brauwere, 1966), in the days of Girardengo, each leg of an omnium contest was classified as a victory but not the GC of that omnium. The reason is that the concept of omnium was not firmly established yet. That's why according to Van den Broeck, Girardengo reached a total of 1083 wins (955 in the track and 128 on the road; I don't know if youth categories were included or not).
Rik Van Steenbergen according to the same author won 1134 races with the modern counts (so only the GC of an omnium included), including 803 on the track and 279 on the road, including 52 races in the youth categories on the road and 47 of them on the track, which means a grand total of 1033 pro wins.
If we used the old method that would compare him to Girardengo, we would have had a grand total of 1643 wins for Van Steenbergen, including 1544 with the pros compared to the 1083 for Girardengo and 955 for Thorwald Ellegaard.
According to Rik Van Walleghem in "Patrick Sercu: Portret van een puzzel" (Lannoo, 2004) and with the calculation of Hilaire Sintobin a good friend of his,
Patrick Sercu won a grand total of 1206 races, including 1015 as pro (914 of them on the track and 101 on the road), 191 wins in the youth categories (124 on the track and 67 of them on the road).
They are both above 1,000 victories and the only two riders to achieve that.