Damage to the sub floor while scraping tile

Fasten your first layer plywood subfloor as you normally should.

The second (top) layer of plywood joints should not coincide with the joists and the second layer should not be fastened to the joists.

Article quote from - Position of Underlayment to Prevent Cracked Tile and Grout By Frank Woeste and Peter A. Nielsen For publication by the TILE LETTER Magazine (read whole article):

The 2003-2004 Tile Council of America’s (TCA) Handbook for Ceramic Tile Installation contains numerous details for a double layer wood floor system supporting ceramic tile. The thicknesses of the subfloor and underlayment are given in each case. Specific guidance on where to butt the underlayment end joints is not given for any detail. For example, for F142-03, the TCA Handbook states, “offset end and edge joints of the underlayment panels by at least two inches from the joints of subfloor panels; they should not coincide with framing below." It further states, “underlayment fasteners should not penetrate joists below." In the case of F150-03, the offsetting is not mentioned, but it does state, “underlayment fasteners should not penetrate joists below." The same holds true for F155; however, it also states, “face grain of plywood should run perpendicular to trusses, I-joists, or sawn lumber for maximum stiffness." The purpose of this article is to propose specific guidelines for the orientation and placement of underlayment, including end and edge joints, beyond the rules given in the TCA Handbook, to improve the performance of double layer wood systems. These guidelines are based on engineering science and field observations.

Also, since you will be using Ditra, make sure to stick with their guidelines for warranty purposes. Specifically see page 8 and 23 from The Ditra Handbook for your application.

One comment on the advice you read is that I don't see a thing in there about deflection - evidently Mike Holmes is sure that if he merely has 1-1/4" of subfloor, all is good. Real tile specs tend to involve a concept called deflection, and that's the distance part of the floor system moves when loaded, relative to the span you measure over. L/360 is a typical spec - L/180 is twice as bad. (It's usually a lowercase L, but on the computer I'm using a capital to be clear that it's an L.) I happen to have a 3/4" subfloor that's L/587, so it really doesn't need another half-inch on that basis.

Consider what a tile manufacturer has to say... (I'm not going to cut and paste their extensive text here, or rewrite it all) but for one thing they specifically mention setting the backer board in a mortar bed, not "gluing" it down. I'd also venture to sneak in that if you really want "the best" (and will you pay for it these days) look at the "old fashoned mortar bed" (TCNA (Method F145-02)) mentioned at the end of their article. That, of course, means you need to establish an adequately rigid base 3/4" or 1-1/4" + tile thickness below the surrounding floor level, which is why it's not popular these days. But it was a VERY good method, as a lot of old houses demonstrate.

Kinsman Tile