Hi ewwink,
According to me using %category% in permalink is definably good Idea. Because nowadays google also takes your url for keywords.
for example if you search “mumbai churches” in google you can see my website ‘catholicchurches.in’ on the results page particularly that ‘mumbai-churches’ category name highlighted in url.
(I could n’t put screen shot here ?? ) . So you can understand the importance of ‘category’ in permalinks. ( I am against ‘Otto42’ on this point)
Solution:
Myself also faced the same issue while using %category%/%postname%,
google said following links had duplicate contents (you can find your duplicate content using google webmaster tools)
https://catholicchurches.in/directory/mumbai-churches/our-lady-of-lourdes-church-sion.htm
https://catholicchurches.in/directory/mumbai_churches/our-lady-of-lourdes-church-sion.htm
the diffrence between two URLs are hypen and underscore in category name.
later I find this plugin which is the best solution for our issue.
https://scott.yang.id.au/code/permalink-redirect/
If you just install and activate this plug in it will automatically redirect the wrong url to the right one. So there is no chance for duplicate content.
Hope this will help you.
Thanks