Most of the time I prefer real filters. The need for NDs and polarizers is obvious, so it doesn't need to be discussed. Diffusion and other creative filters I use in camera out of three reasons:
First, I want to give the director, the editor and the production as early as possible the impression of how the image should look in the end. It is a psychological thing: If editing takes a long time, directors get used to what they see working with the rushes. So sometimes it can be difficult to bring in something new in the end. (Sidekick: This is also a reason, why it makes sense to make rushes already with a custom made LUT instead of only Rec709 (or even worse: without any LUT at all).)
Second: Sometimes as DoP you can't join the color grading (mostly in commercial work). Especially in this case I try to keep as much control over the image as possible by using glass filters. And I also use graduated NDs. Besides technical reasons (contrast reduction) I want to give the image a character/mood already on set.
Third (and fourth): It saves time in post production and most important: mostly it looks more natural.
Sure there are exceptions: if you shoot for VFX, stay away from (creative) glass filters. Every VFX artist who should key a greenscreen that was shot with diffusion would kill you (justifiably). Same for stereo 3D. Slightly different effects of the two filters could blow your 3D.
Second exception is, if you get reflections or ghosting from too many stacked filters.
Using glass filters requires one precondition: you need to know the filters very well and how to use them. Same filters look different on different focal lengths, types of lenses and with changing conditions on set (haze, backlight, frontlight...)
But once you got used to it, it is so much fun! I love it.
Here is a very good comparison of Tiffen diffusion filters: https://vimeo.com/tiffencompany/4kdiffusiontest