You shouldn't overestimate the impact of penetration on indexes. After all the true count does already allow for this.But deep in the deck the true count will be altered more easily with a newly drawn card causing a slight change of the ev-situation. Not a big deal though.
Of course I don't use different indices for different penetration levels, nobody does as far as balanced counts are concerned.
I get my indices with the infinite deck method and I'm confident that for shoe games they are very close to the weighed average obtained by other more complicated methods that T-hopper referred to.

Francis Salmon