Hi Ckelgo,
Can you upload a photo or two of your Hoya so that we can get a better idea of what might be going on? Do you know which particular Hoya you have? Hoyas in nature grow on trees and their long vines cling to and climb the tree, so long stems are not at all unusual. Some people who grow Hoyas as houseplants, place moss poles or some type of trellis structure in the pot to allow them to climb, while others grow them in hanging baskets, allowing them to trail downward. Misting isn't likely doing much but it doesn't hurt. The important thing is the potting media; Hoyas need a light, airy potting medium that allows for good aeration at root level and perfect drainage.
It's fine to prune stems, that's how most Hoyas are propagated for additional plants; the part you don't want to prune off is the peduncle (bloom spur) that resembles a little microphone. Sometimes the bloom spurs will abort/fall off for whatever reason but it's never advised to prune them because that's where new buds form. You can see the peduncles, annotated in my database photo below.