Can I use old bowling alley lanes as counter tops?
I don't have direct experience but generally speaking while a circular saw blade can go through nails, it's dangerous as it increases the risk of a kick back.

Although slower, you will be far safer if you cut the counter using a reciprocating saw with a demolition or dual wood/metal blade attached.  That will cut through nails without the kickback potential.

You should cut your pieces a bit wide, say 1/8" extra, since your initial cut very likely won't be perfect.  After the initial cut, you can sand the edge down to fit.