Even if you could drill these holes, how on earth would you thread the waste pipe through them?  (don't say cut the waste into 12" pieces and use lots of straight connectors   )  However if that's what you intend then drill between 0.25 the span away from the wall to 0.4 the span away from the wall, drill the centre of the joist depth and max hole size is 1/4 joist depth. (in your case 56mm)

You could notch the top of the joists.  There's a link somewhere here to tell you where you can and cannot cut notches but generally between 0.7 to 0.25 of the joist span is the area you can notch from one end.  The notch depth must not exceed one eighth of the joist depth.  So a 9" joist allows a max notch of 28mm!

Could you not run the pipe above floor level and box it in?
Surely a lot easier and safer!!

What floor covering are you going to have?

If tiling you could notch the joist 25mm, leave a gap in the floorboards above, say 20mm. This would just give enough clearance for a 40mm pipe, then run your ply and tiles straight over the top.

OK for short runs but may not give the fall required over a longer distance.

Jason