Like Kirk said if you are using a flat table cnc nested base machine, you will need to get a horizontal boring machine, most of which also glue and insert your dowels in the same process. If however you are going with what is called a PTP (Point To Point) machine or sometimes called a Rail & Pod Machine most of them have at least 1 drill bit usually 2 that will drill horizontally in both the x and y axis.
I have never worked anywhere using a flat table nesting machine, and have only used PTP type machines. My experience is even though you can drill horizontally it works much better to have a horizontal boring and dowel inserting machine.
These horizontal machines come in different setup, some have a lot of drill bits set at fixed locations. The other type has just 1 bit and insertion tool. This will move left and right to any location you program into it, and even though it only has 1 bit it moves pretty fast and covers the same area as the machine with several bits. In my opinion this single bit machine is much more practical than the multiple bit machines. (Not trying to start an argument just stating opinion so my apologies to those that prefer the multiple bit machine)
I Hope this helps.
Jim Smith: