I'll be in Guilin next week for 3 days. I have yet to decide if to stay in Guilin city or head out to the smaller villages.
The reason for my visit is to shoot landscape photography of the karst mountains, the Li River and the Cormorant fishermen that fish in their bamboo rafts(at sunrise). I'm also looking for sunrise/sunset spots where I can get good views (weather permitting) of the karst mountains and the river. Any recommendations on where to stay and hiking trails for sunset/sunrise will be appreciated.

Definitely do NOT stay in Guilin. Whether you are a tourist or a photographer, Guilin offers very little other than a train station and an airport. When you arrive get out to Yangshuo ASAP and stay out there.
The Yulong Scenic area is close off for private vehicles except scooters/bicycles since sept 2017, u can rent electric scooter to gain access

Great, thanks. At which do I find the Cormorant fishermen that fish in their bamboo rafts(at sunrise)?
Hopefully the weather improves, but I know there are no guarantees

I land at Guilin airport at 21:10. Is it still possible to go to Yangshuo at that time by public transport? Perhaps better off staying that night in Guilin city.
As Chinese cities go, Guilin isn't base (Quite nice, in fact). It's just that what it has to offer (And it does have a few tourist attraction of it's own) aren't the things that draw people to the area.
I once did the boat trip down the Li River (On, it turned out, one of a fleet of massively oversized boats). It was awful and I learned later that the best idea is to rent a raft and "driver" in Yangshuo and go off up one of the Li River tributaries. There you might expect to see cormorant fisherman. I certainly don't recall seeing any on the "cruise" (I have seen cormorant fishermen at quite close quarters. But on the Yalu River that separates China from North Korea).
I've only ever stayed in hostels in Guilin and there are a number of good ones. But, perhaps, you're looking for something more up-market.