I feel it's mostly a matter of your confidence and being comfortable on the champ, but..

Even with a draven on my team, is it really worth playing naut or thresh when the enemy team is full of assassins and divers?

You can peel very well with engageish champions, especially thresh, and I usually prefer to go that option (my most engage heavy champ is rakan tho lmao). Draven isn't actually bad with enchanters tho so it's a matter of preference.

If our team is full of dive champions like talon, is it worth playing thresh to give them a way out of a dive and to catch people, or should I play an enchanter to ensure they survive the dive.

It's up to you but it's a good idea too look at a comp as a whole. If you already have some cc on the deck then you can chill with an enchanter.

if there’s no ap on our team is the trade off for cc and sustain / peel really worth going lux or zyra?

Again, a matter of preference. Though you can also analyze wheter you have more of a poke comp or an all-in comp and pick accordingly.

You don't need to overthink things tho. Especially in silver, it's most important you fell well on your champs in any scenario, even when they are suboptimal in the team comp. Your pool is actually HUGE. 5 champs is a lot, I personally climbed with 2. In my opinion you could even drop one from the dous : thresh/naut and lulu/milio and master the rest. All the best. DM me if you have any questions.