Playing small pocket pairs 100 bb deep is very profitable. The two glaring problems I see with your question are calling large bets/3bets pre-flop, and playing passively on the flop when you hit your set. You may also want to re-evaluate your thinking about three bets usually being made light, and how you react to them when they are.
Players will gladly stack off with their over pairs and top pair hands if you have given them a reason to believe you do not always have the nuts when you ship it. Many will auto ship over pairs and top pair, even at higher levels. Tight players in particular love to get in with AA and KK on the flop. With this in mind, set mining can be profitable in most games if the price you pay is generally small in relation to the stacks. Most of the time you are looking for very good implied odds
- not just because you want to win a stack, but because many times you will only win 1/4 of a stack or you will lose to a better hand than your set. Most skilled players use guidelines of 2-5% of effective stacks as the maximum you should risk with speculative hands. If you have multilple opponents you can loosen that requirement because there is more money in the pot pre flop and more people to pay you off if you hit. Cold calling 6-7 bb pre flop with a small pp is a losing proposition. Calling 3bets with these hands is even worse; the pot will be so large that your opponent will almost always be getting the right price to get all in on the flop with their good hands and they will often check/fold missed high cards. Your small pair loses in both scenarios at 100 bb stack sizes.
One of the biggest leaks casual players have is playing strong hands weak for fear of chasing off strong, but 2nd best hands. Very rarely is it a good idea to slow play you strong hands. The same player that c-bets 2/3 pot on the flop then checks the turn will often call large bets and check raises on the flop, then fold the turn. Sometimes they re-raise all in on the flop. If you think a player is sneaky you can really use bet sizing to wreck them, but usually just playing aggressively works best.
As far as 3betting usually being light, it just is not true. Some players will 3bet alot, and then maybe your hand is good enough to 4bet with, but in general, even their weak hands often have substantial equity against a small pocket pair. Calling the 3bet with a small pp is just never a good option at 100bb deep. Not only are you likely losing badly or slightly ahead, but they have the lead on the flop and will win with a bet very often.