I'm not entirely sure why, but in basically every version of the game I've noticed a loss of FPS as the fortress ages, even in a fortress with only one dwarf it will eventually slow to a crawl compared to what it was at embark.
If I had to guess, I would think it's because the game has to keep track of everything, the longer a fort exists, the more stuff there is to keep track of (as animals come and go, stones get excavated, caverns and water are found, weather and temp changes if they're on, politics and relations with your neighbors, the piles and piles of corpses you'll probably have after a few years. Even if you don't seem to be doing much, the number of things the game needs to keep an eye on grows pretty rapidly.
A few tricks to help this is to make an atom smasher and dispose of anything and everything you don't need, even this won't free up your FPS entirely but it can buy some more time before you're in 1FPS. Also close off useless paths (wall them off) so they wont be considered for pathing calculations. Cage animals, kill wild animals, if there is any water (there probably is) try to keep it from having any flow, ditto for magma if you can manage it.
Beyond that, there will still be a steady drop in FPS for whatever reasons, it may be that there is more the game tracks behind the scenes than I am aware of, maybe it's just some issues with optimizing the engine, I've found nothing to prevent this.
50FPS is actually very high, though, in my experience. Freshly embarked in the 2D versions of the game when I still had a windows partition to play it on, I started with 50FPS and it declined from there. My current fortress in the newest linux-native version is running at 10-20FPS(depending on number of idlers mostly) (111 dwarves, ~5 years old, all cavern layers etc breached and open, running water, etc.) It started at 98FPS at embark