Let us say I have TracksA.tck and TracksB.tck, and apply tck2connectome to obtain two matrices based on a given parcellation.

Is the sum of those two matrices equilavent to the output of tck2connectome applied to a tck file created by merging TracksA and TracksB tck files?

As long as the edge-wise statistic used when generating the connectome for each sub-tractogram is “sum” (which is the default), then yes, that is equivalent.

To explain the clarification: Imagine you are interested in the minimum streamline length between each pair of nodes. So for each edge, tck2connectome internally tracks the minimum streamline length of all streamlines assigned to each edge, rather than “getting the streamline count”. If you were to do this for two separate track files, then taking the sum of those two matrices is no longer the appropriate thing to do.

As secondary question, is there a way through mrtrix commands to merge multiple tck files?

Yep: Simply provide multiple input images to tckedit.