You'd be very surprised on how much accuracy with your cutting affects the overall quality of your build. If there's too much excess around the tabs, parts might not fit together well and eventually you'll end up with a badly-shaped piece. The same goes for edges - if you cut too much off, or perhaps not enough and there's excess, you'll end up with similar problems later on when all the little faults add up.
Honestly, the best tool to use in cutting out your pieces is a craft knife/Exacto knife, paired with perhaps a metal ruler if you're not confident about running those straight lines without some guidance. Try to cut just on the line as opposed to outside or inside it, and if it helps, you can set the print quality in Pepakura to 'high quality bitmap'. This should give you nice, clean, thin lines that are easy to follow, but reduce the amount of problems that could eventually affect your build.
End result: a professional build, without your hands aching, and much less waste paper pieces strewn about your work area.
Not to say that scissors don't have their place - I prefer to cut extremely large pieces out with a decent pair of tailor's scissors, specifically support struts and the such where accuracy isn't so vital.