Direct deposit and paying amount due by check

Yes and Yes but you might want to inform clients of the pending change and encourage electronic payments.

IRS has issued something about not wanting to issue paper refund checks and how they will be delayed.

What part of "The Secretary of the Treasury, shall review and, as appropriate, revise procedures for granting limited exceptions where electronic payment and collection methods are not feasible, including exceptions for individuals who do not have access to banking services or electronic payment systems" do you not understand?

The taxpayer is your client, not the IRS.  It's fine to order the Treasury to do something "as soon as practicable, and to the extent permitted by law."  But taxpayers have not been ordered to do anything, nor can they be.  

While the program by default does still generate the vouchers, you can turn them off within returns.  To do so follow these steps:

1) Go to "General"

2) Go to "Misc Info/Direct Deposit"

3) Click on the "Miscellaneous" tab

4) Scroll down to the field "Form 1040-V: 1=when applicable, 2=suppress"

5) Enter a "2" and ProConnect will not generate the 1040-V (payment vouchers) in the return.