I received job offers from 2 different companies. When I got the offer
from the 2nd place (a startup), I got emails from most of my
interviewers (potential coworkers/colleagues) and from the Tech VP
wishing me congrats and expressing their hope that I join the company.
I've decided to go with the 1st place, but I haven't told the startup
yet. I'm not sure how to reply to these emails.
When it is the appropriate time to decline their offer, contact the company in the way their system specifies. It could be an email, or it could be via their job candidate system.
Do I reply to each one (before I decline the offer) thanking them and
letting them know that "I'm deciding between 2 offers, and I hope our
paths cross again the future if I go the other route"?
There is no need to do this before you decline the offer. If you are undecided about which offer to take and you need more time, it may be possible to extend their offer timeline by contacting a specific person involved in the hiring process. This shouldn't be done by responding to all the other emails.
Or do I wait till I decline the offer, and then reply to the emails
thanking them but letting them know that I've decided to go a
different direction?
Once you have declined the offer, there is no need to respond to most of the emails. I would only contact somebody if I already knew them, or reasonably expected to see them again.
Or do I reply with a simple Thank you and not say anything further?
I would ignore most of the emails. Those who need to know about your decision will be informed by the company. Those same people may now be deciding if they want to notify the next candidate or start the process again.