Actually I am into a fairly similar project, namely, hacking a Ghielmetti (EMS AKS style) matrix for use with the Axoloti (or if that should hit performance constraints as a controller for some yet to be determined crossbar).
Crosstalk is a general problem with analogue matrices - it generally was reduced by using resistors in the pins or cables, but the EMS synths (as most prominent examples of the matrix paradigm) still owe much of their appeal to the fact that they grow increasingly random once multiple pins across rows and columns create a back and side flow of the signals.
My solution to the problem is to use the matrix as a digital input device (as originally intended in its industrial applications), with diode pins which eliminate crosstalk entirely (when used with unipolar control signals). Of course, that leaves the task of mixing the signals to the software - which might create excessive load on the Axoloti depending on which signals you want to mix.
A multiplexer will give you more input lines to one single input, which is something you may need if you run out of I/O - but it cannot replace the matrix (or emulated matrix) by itself. If you want to go all analogue, careful selection of resistors and buffers will be the way to go - but that will be very much a matter of trial and error.
