Any unused open knockouts must be plugged. The plugs are ten for $1.
There are rules for "box fill" in which the wires and devices are counted and compared to the box cubic inches (which is stamped in the box or a standard book size).
This type of 1-gang "Handy-Box" has just enough legal box fill for 2 wires in, 2 wires out and 1 device/yoke. You don't have room for more wires also.
Every wire transiting through that box will add 2 cubic inches to the box fill calculation. So your plan isn't going to work with these little 1-gang Handy-Boxes... (unless you put no devices or splices at all in them, in which case they follow the same rules as a conduit body: if it fits in the conduit it fits in the box.)
Also, as a practical matter these boxes are too tight to comfortably fit an AFCI or GFCI receptacle in - and I'd remind you, if a circuit needs AFCI and you have EMT metal conduit to the first receptacle, you're allowed to use an $18 AFCI receptacle instead of a $40 breaker.
What you should get in the habit of using, instead, is a 4x4 metal box with a 1-gang "mud ring". This gives you the spacious room of a 4x4 box + the mud ring, or about 26 cubic inches between the two - double the Handy-Box.
If you need even more than that, 4x4 "deep" boxes (2-1/8") are 30 cubic inches, plus the 5 for the mud ring. If you need more still, they make super-deep boxes.
These boxes have plenty of elbow room, both for thru wires and for AFCI/GFCI devices.
With mud rings, you mount the 4x4 box flush with the 2x4 stud (or even up to 1/8" shy of it) and then the mud ring protrudes through the drywall.
These boxes with flanges can be a bit specialty (at least, in the rest of the country) and the big-box stores tend to overcharge for rare stuff... a real electrical supply should be more in-line.
You might need to trim the conduit slightly for a 4x4 box, since it is flush with the wall, not proud by drywall thickness.