Three questions for you pros

[Fyron]

In the long run, the savings from not having to build space ports is not worth 1000 points. Spend those 1000 points in your Minerals Aptitude characteristic, and you will get far more benefit out of it. Or spread it around a bit to other resource characteristics and research, and you will still get far more gain overall as compared to selecting Natural Merchants... Natural Merchants was neutered from how it was in SE3, where it took 10 turns to build a Space Port on a new planet (and there were no "characteristics", just "advanced traits"), and there were far fewer facility slots in systems overall. In SE3, it was practically a must have trait. In SE4, it is fairly worthless except in contested border systems, which tend not to make up much of your empire... Hence the 8 turn build times in Adamant Mod that Aiken refered to. If you are overly worried about losing your Space Port planets, just build 2 or three Space Ports per system.

[Alneyan]

Also note that Emergency Build allows you to build these Spaceports in a mere two turns, at no cost if the planet in question has less than 10 slots.

The main use of Natural Merchants is to be safe from losing your spaceports in a given system, and even then it is only useful if you have a low number of systems (for example, in NGC5, four Empires had a single system at their disposal, with an insane number of good planets. But if these Empires forgot to build several spaceports, it would have been very easy to shut down their whole planetary production with a single offensive).

If you have a big Empire, you will either not feel the loss of a single system, or you will suffer from massive unhappiness if you cannot defend yourself, resulting eventually in the dreaded riots. Once 95% of your planets are not producing anything, being safe from "spaceport loss" is of little use to your collapsing Empire.