Using unupped hourglasses does pull down the win-rate, but not as much as using 6 unupgraded hourglasses did in SGbow.
Well, there isn't really a way to play it wrong unless you're starting your shield chain too early/late or playing early creatures before you'e drawn a quintessence.
The win-rate has probably gotten lower, but it should be nowhere near 0%. Maybe you could keep track of which gods you're facing? Half of it may be you being unlucky in which gods you meet.