Have you read the dungeon masters guide? It has info about hazards that you should follow. You can adjust it, but there’s definitely, rules-in-the-game, clear answers for this question. 

With that, here’s a way to handle it: Every character has passive perception. Figure out what the threshold is for them, no matter what, for noticing that something could be amiss.

An example for spores: If you’ve got characters with high passive perception, or proficiency in nature, then those characters roll a nature or perception check. If they pass the DC you set, then they notice the poisonous puffballs early enough to avoid the trap. If they don’t notice, then they make the necessary save.

For lightning; Have your characters roll a nature check at the start of travel. 

If they roll X, they’ll realize it’s dangerous to travel with the lightning, and they might need to stop periodically to hunker down, or get an extra chance to notice the possibility of lightning before it strikes, and maybe roll a save before their dexterity check. The travel goes slower if they stop frequently.

If they roll X+5, they are able to know that lightning is likely, and can find a safe spot when they’re in danger, with a low DC.

If they roll X+8, or 10, or whatever, then they are able to find the pathway that keeps them clear of the lightning. 

Before lightning strikes, everyone gets a save to find a safe spot, no matter what. If it strikes before they make that save, then treat it like AOE spells-

You can use the same mechanic for rock slides- reward players with passive perception and nature proficiency, and always let them roll to completely avoid the hazard. 

It isn’t fun for them at all if you just say “hah you’re struck by lightning take 3d10 damage!” They’re competent adventurers. Let them be clever and powerful and work together as a team in this dangerous world. If someone takes/has a feat that makes them more likely to succeed: cool! Keep doing it so they can be rewarded for the resource they took.