Will the Social Security Administration accept W-2's and W-3 printed from Quick Books?

Yes. A big company like Quick Books would make sure the IRS would accept their printed forms.

Of course, the easiest way to be sure is to EFILE the W-2 and W-3.

I worry about the thousands of fraudulent tax filings recently, those getting refunds.
It takes the IRS quite a while to match the filer's W2 with the employer's.
Yikes

Yes; that has been a longstanding problem that the 60 Minutes expose has brought to light.

Not sure how it can be resolved, even with electronic filing of W-2s.