I have body side molding installed on my EX. I added them by default because older Hondas used to come with them standard, and I wanted them for extra protection. The dealer installed mine as part of purchase, but you're right that the installation instructions don't look so bad if you have the right tools available.
The molding has a VERY flat profile (compared to older Honda standard). They provide some protection, but seem limited since they're not very deep. I also don't 100% love how they look on the car. They're body-colored but still stick out to my eye because it distracts from the 'smoothness' of the side profile. My car looks 'sportier' because of the extra angle attached on side, but I think I prefer the 'smooth' look.
Net, if I had to do it over again, I'm not sure I would have added the body side molding to my car...