Do Shadow Achievements Count In 40 Achievements Run?

they do in earlier versions; any achievements that count towards the total achievements number on the stats page are allowed. in later versions shadow achievements don't (i dont remember exactly what version it was changed on, if you want to know check the wiki) however in earlier versions they do

So if shadow achievements counted in previous versions, but new achievements were added to the newer version which one is faster?

1.0466 is faster for 40 Achievement