The same principles of glass cutting are applied to fused glass as to the glass used to make the fused piece. The differences relate to thickness and variations in thickness.
You still score on the smooth side. More pressure is not required. For glass thicker than 6mm, you may wish to use a wheel with a more blunt angle. as shown in this illustration.
The main reason that people may feel it is difficult to cut fused glass relates to the additional thickness. Just as breaking 4mm glass requires more force than 2mm, breaking a 6mm piece requires more force than a 3mm piece.
Properly adjusted metal cut running pliers can do the job, but a cut runner designed for thicker glass can be a boon. They are designed to provide greater leverage and so more force to the glass breaking. With these the glass breaks along the score line cleanly.
The breaking of glass that is uneven in surface levels, as in tack fused pieces, can be more difficult. One is that running the cutter over glass with distinctly different thicknesses can be difficult. Maintaining consistent pressure and speed over the bumps of the tack fused pieces is difficult. The second is that the running of the score will not always follow the score line. For example, if the score line runs close to the edge of a thick piece, the break is likely to skirt around the thick piece, and possibly off to the edge of the piece, rather than continuing to follow the score line. Planning the score line on tack fused glass is important to avoid trying to break near the edges of thick pieces.
One possibility is to score the glass on the shelf side. This is certainly possible, even though the surface is rougher. It does avoid scoring across different levels and makes the break along the score line more probable.