I'm not aware of any research that would indicate how most churches handle their payroll, but my guess is (just from personal experience) that most churches pay their pastors using a physical check. That's how our church operated for years. I was paid once a month, at the end of the month, by physical check for six years.
Most of the time, that process worked fine. Some months, I might get paid a couple of days before the end of the month; other months, I would get paid on the last day. However, on more than one occasion, I was paid late.
I remember one time in particular when our financial secretary had an emergency in the family right at the end of the month. She immediately left to be with her family and did not come back for a week. Since nobody else in our church at the time knew how to process payroll, what that meant for me was that I did not get paid until the 5th of the new month!
The uncertainty of this method eventually led me to begin looking into direct deposit options for our church staff. Since we use Quickbooks for our bookkeeping, we decided to use Intuit Payroll's direct deposit service. At only $1.75/paycheck deposited, it is an affordable and easy-to-use solution for churches of any size.
Now, payroll is a breeze, and we always get paid on schedule. I LOVE it.