This really is one of the more ridiculous Clinton campaign talking points that just made them look very out of touch.
Pepe is a common meme template. Of the thousands of Pepes that I have unwillingly seen, none were neo-nazi except those in articles accusing Pepe of being a neo-nazi symbol. However, if you go to a deliberately offensive chan then sure, you will find every meme-template being used offensively.
YMMV. In the circles I browse, they are frequently used, but they were only used to troll. They are certainly used for more aggressive hate in other places, including on Twitter.
Your samples are biased there. If you are already looking at alt-right tweets then obviously you will see more trump- and nazi-related pepes.
If you look anywhere else then pepe is just another highly versatile meme.
/pol/ also shopped MAGA cap onto various anime characters. Momiji inubashiri being particularly popular, probably because she already wears a red hat in her canonical design. Does that mean those anime characters themselves symbolize hate or even conservatism? I think not.
It just means that outside observers are not familiar with memetic mutation.
He went from "Feels Bad, Man" comics to being very frequently photoshopped with 3rd reich / swastikas / other neo-nazi logos.
Pepe is an interesting case because it brings up the discrepancy between trolling (messing with others in "bad fun") and actual people who vehemently support and push aggressively hateful messages.