The smite mastery is only 10gold per smite and after early game you are saving smite for big objectives so is it really worth it to use one point for what really amounts to one ward around the 8 min mark that you would not have been able to afford otherwise?
Smite has a cooldown of 70 seconds. Baron takes 7 minutes to respawn, the dragon takes 6 minutes. This gives you 6 smites within a 7 minute time span, or 4 extra smites you can use whenever for a free 10 gold. Knock out one of the siege minions in a lane, kill a random Golem... all cases where you'll also get some free gold. As the cost is an ability you can't even use in team fights in most cases (barring Annie and others), it's essentially around 120 free gold or more in the period between objectives. Even a farmer who would already get the kill, it's still an extra 10 gold for virtually no significant cost - it's fast, you barely need to travel, no mana cost.
It's not a lot, ultimately - it translates roughly to the equivalent of 1.4 gold per 10 seconds if you were to fire it off every time after cooldown (and ignoring the periods in taking down the objectives). But it is pretty effective and can give you a pretty penny, so if you have the spare mastery and are going with Smite to begin with, it can be very functional. Just realize that you can toss it out around 4 times between objectives, give or take based on the obvious desync for Dragon/Baron spawns.
If you need to put points into the mastery anyway for another spell or if you need points in the tree for the rest of the masteries, then it's not a bad idea to take it. You're right that it doesn't net much gold, but sometimes that few points of gold will help you in the end; getting an item finished ahead of your enemy will usually make a huge difference.
The extra gold helps, and the jungler still tends to be less farmed than his whole team except for the support, unless you feed yourself off ganking. Besides, the defense mastery tree is good for junglers, and Magic Resistance isn't really needed to jungle. The 2 Magic resist you would have lost is almost negligible in all situations. This assumes you are speccing your masteries to jungle and chose 3 in the armor mastery.