You're already using uint8 to store your values. There isn't a smaller type unless you start packing booleans into bits which I assume is not possible for Xfreq_last anwyay. Using bits to store boolean is bound to be slow in matlab and awkward in matlab. There's no built-in function for that.
However, your storage looks incredibly inefficient to me. Say you're processing the first word of the first document. You find it in documents 2, 10, 150, 2048, 4125 for example. For a start, instead of storing those values (which woudln't take much memory, ~20 bytes as uint32), you store a boolean array of size 1x5549 (~5549 bytes) with only a few ones. But more importantly, in document 2, you're going to be looking for the exact same word, which you'll find in the exact same documents and store that again. Why?
Why not do the storage per word, instead of document, and for each word, just store which document it's found in?
