You have full control over which clients see or do not see the option to use Joist Payments for credit cards and E-checks.
You can turn the default payments options on or off, which would determine whether or not each subsequent estimate or invoice you create has payments enabled.
You can find this option in iOS by tapping More in the bottom right corner, in Android by tapping Manage, then choose Payments. There's an option for Credit Cards and another for E-checks.
You can always choose to turn payments on or off on a specific estimate or invoice using the payments switch in the edit screen for that document -- this choice affects only that document.