Mastodon faces all the same challenges, and has been dealing with them for 7 years.
Unfortunately, lemmy comes with some bad default settings for when you set it up, which is the cause of the current bots inflating the user-count.
As for how to tell if an instance is trustworthy... That'd be time. I picked mine because it's local and has had years of uptime already. lemmy.world is new, but run by people who've maintained a mastodon instance before. Basically, do your research, and wish for the best. Eventually, some day, we'll have established no-brainer options like gmail and proton are for email.
Monetization, that's up to each instance admin. Mine is straight up donating the instance to the world, and not asking for donations due to its near-nothing running costs. My instance is quite small, but active. But really, a given instance could go with whatever funding model they want, provided its users are on board with it. Some have already told our admin to speak up the moment he'd like some funds.
Where malicious activity is concerned, the fediverse may have to eventually switch to using whitelists, instead of blacklists, for who they federate with. Aside from that, there are already some tools for automatically detecting instances that are not populated by real users.
On privacy, ActivityPub has none. For that, you should look to matrix. ActivityPub is for public-only interactions and has no guarantees of security. Your posts or comments are not DMs, and if you reveal personal information, you may as well have published it in a newspaper. There are no real take-backs in that kind of forum. You can have facebook or reddit delete your stuff under GDPR requirements, but your content was out there, and any saved copies are out of reach.
The same goes for deleting things on the fediverse. ActivityPub does have the featureset for it, but it can only reach server's that are still online and federated. That's little different from how other public social media works.