The software is from your hosting company, right? They already have access to all your stuff from their end, right?
Sure, you could have a hacker break into your computer and get to your stuff through that program. However, they can just as easily install a keylogger and get to your stuff through the web. The disclaimer in that software is probably the same or very similar to the disclaimer in the TOS for your hosting.
The bottom line is that the software gives you quicker & easier access to manage your website, but if you can’t sleep at night due to worrying about it, then that convenience may not be worth it to you. Go with your preference and don’t worry so much.