Can I run two cables through the same conduit?
TL;DR -- go right ahead

This looks to be a sound plan -- it's definitely cheaper than running everything in conduit, and probably somewhat easier too even with having to stuff two NM cables down a 3/4" EMT length.

Fill isn't an issue

Even though the Code conduit fill criteria don't apply to protective sleeves, you're fine on fill (albeit barely).  Encore Wire quotes .160" by .450" for their 12/2 W/G NM product -- multiplying and converting to mm^2 gives us a conservative area estimate of 46.5 mm^2 per cable.  Doubling this to account for the doubled run gives us 93mm^2, which is within the 106mm^2 (31% 
 fill) available for two wires or cables in the 3/4" EMT.

Nor are derates

Normally, since you have more than 3 current-carrying conductors in the sleeve, you'd have to derate as per 310.15(B)(3)(a).  However, this derate starts with the 90&deg;C column in Table 310.15(B)(16) as per 334.80.  Since we are derating by a factor of 80% for the 4-6 conductor case, we get 24A derated, which is above the 20A 60&deg;C ampacity that's actually used for the cable as per 334.80, so we're good on that front too.

And the EMT is suitable

NEC 334.15(B) states that EMT is one of the allowable means for protecting NM from damage in an exposed application.  PVC can also be used, but it must be Schedule 80 PVC -- the cheaper/wimpier Schedule 40 stuff just won't do.  There shouldn't be any concerns with impedance, grounding, or the likes either -- protective sleeves are not required to be grounded or bonded as per 250.86 Exception 2, and it's grounded anyway via being connected to a grounded metal box.