MATLAB DAQ is very good (I wish the open source MATLAB clones like Octave and FreeMat would have something similar :) ). We were using it with several acquisition boards without problems. It is very configurable, so it's quite easy to enable data reading from completely new hardware.
If that DAQ toolbox still doesn't do the job for you then there are other toolboxes, like Instrument Control Toolbox that offer other type of communication protocols too.
But are manufactures still doing this or is or has the MATLAB toolbox lost popularity?
I don't think MATLAB (or any of it's toolboxes) lost any popularity :).