There are three options that I see for you.
1: Keep doing what you're doing. Fill the crack, finish with another thin coat of varnish, and see what happens. Maybe it cracks, maybe it doesn't: If it does, fix it again.
2: Embrace the possibility of cracks and work around it. Refinish with an oil finish so that a new crack won't really mar the finish like it would mar a glossy finish. It'll just look like the crack was always there and may not require your attention to fix.
3: Do more to eliminate the possibility of cracks. Finish both the top and bottom of the slab with a thick coat of clear epoxy. This won't guarantee no cracks, but it will dramatically slow down the rate at which at the moisture content of the slab changes, which is what causes the cracks in the first place (I believe). With this option, you MAY prevent further cracks, but there's no guarantee, and fixing any cracks will likely be more time consuming.
I don't think there is a perfect option, because working with slabs like this is fundamentally tricky. In the end, you're going to have to take a leap of faith and be willing to fix it if necessary.