It's not uncommon that film and media composers have huge 1000+ track templates. I started building my own and while the template project grew and grew, Studio One got slower and slower. Here are a few things that used to take under a second, and now will take 5-10 seconds.
1) Adding a new track
2) Adding new outputs to instruments.
3) Scene switching is unusable (takes too much time to load the tracks)
4) Unsoloing (This one is weird. If I have a couple of instruments soloed in my 1000+ template and use the "global unsolo" button it takes a loong time, but using the instrument's solo buttons those unsolo immediately.
5) Maybe because of the number 4 point, the extract to audio takes HOURS! I have a deadline today and I've been sitting and waiting to get my mix project up and ready. I have used maybe around 50 tracks of my big template, but it is still going :/
My PC specs:
i7 6700K, 64Gb ram, Win 10, using SSD drives.
The latest version of Studio One 3.5
I use Vienna Ensemble Pro 6 (latest version) for hosting Kontakt and Play samples.
With Cubase, you don't see these kinds of slowdowns, so I'm afraid it is just a matter of optimizing the Studio One to bigger templates and how it handles large track count.