You're needlessly increasing your variance. Let's say on the first hand everyone gets a twenty or blackjack. You miss that hand and come in later. You see a lot of low cards and think the count is high, but it really is close to zero, so you're max betting for nothing.
You have to count all unseen cards as behind the cut card. If 1 deck has been dealt out of 6, when you join, you divide the running count by 6, not by 5.
Just wait till the shuffle, claim that you don't want to mess with the "flow", ploppies do that all the time. Or come in mid-shoe and randomly vary your bet till the shuffle for cover.
Of course the best way to deal with this is just to wait at the table for a shuffle.
If you must, see how many decks have already been dealt and consider them as still in play. 4 deck game, one deck already dealt when you sit down. RC hits +12 about 1 deck later. Instead of dividing by two decks, divide by 3 as you did not see that first played deck.
Of course the best way to deal with this is just to wait at the table for a shuffle.