Absolutely change that boot, it was one of the first things I did after buying my used GSXL. Even the OEM boot would fail in short time, especially if work was done that required removal of it. I have seen a few that leaked when they were new.
It was far more reliable than the Kawasaki offering of the day though. The old ZXi's had the trim motor placed inside the main electrical box, the cable grommet would fail in the aft part of the ski, allowing water to travel and literally fill the electrical box. So, with a live hot planted in that box, massive electrolysis would ensue, fuses blowing in a different location and all that. Brand new skis would suffer major electrical failure. Then when you opened the box, water would spill and the strongest, most foul odor would emit and seemingly never leave the machine. All for a little grommet.