It's bugged.
I submitted an issue but they don't seem to have understood it. 

I destroyed a +capacity resource thinking I had two, could no longer build my designs with just 1.

Having them limited to one per player doesn't really make sense though unless something is added so you can see how many you have. (Except on the trade screen) 

I don't think it is bugged.  It would be weak to have them as trade items if you could only use one of them.  I think it is just a leftover tool tip.  It would be nice to have a handy display outside of the trade dialogue. The trade dialogue has a mechanism built in for trading multiple copies of a supposedly one-per-player item.  I can offer you two or more of any of them.  That is why I think it is working as intended, but documented incorrectly.

... that's still bugged, tbh

But yes, they make infinitely more sense as stacking bonuses. They need an aggressive nerf, though. 

Even without abundant settings, some give out 10% global increase to stuff. At a time when the interface is being butchered to try and cut overproduction, one might argue that massive global bonuses for colonizing Craphole 1 are a great candidate for nerfs.

Currently I am in a protracted war with they Yor. I have 38 colonies, they have 29.My global planet settings are uncommon as well as resources. It is turn 386.  I am power level 2450,  they are power level 2440, at one point they were higher. The rest of the ai are about 100-300 points below us. 

Regarding the resources we are discussing I have on average about 3-4 of each one EXCEPT , the tourism ones which I went and bought up from all the minors and other majors simply to boost cash so I could rush buy stuff. I am doing about 2100/bn per turn and my production prime is 540 for the capital and 280 for its neighbor planet. I am cranking LARGE hulls out ever other turn. I have not reached Huge yet. 

Over all they (the stack-able resources) are nice but so far are not the tipping scale unless....you grab many 8+, which equates to 40% increase in whatever: Movement, or economy or happiness.