You normally make more money then your hirelings upkeep but you'll never earn back the cost of the upgrades.
The most convenient upgrade is the Botanic Garden. Together with the Curioso shop and the Warden it's the only one you actually want. The Inn was a bit dissapointing. If it gave you all resting bonusses instead of one it would be worth it, sometimes, but as it is there are much better inns in the world. Some even increase you're stats by 6, the best you can get in your own inn is +1stat and +1skill.
As Varana said, it was a stretch goal and it more or less, serves it's purpose.