Link to the gallery of pics:
http://imgur.com/a/d67Vw
So here are some grabs I took of his demonstration for the 'upgrade bug'.
You can see a lot happening here.
First - white circle I think means core tech upgrade level? I'm not 100% sure. However, you can see there is sometimes a relationship between the highlighted colour of a grid of equipped upgrades and the stats to the right, as seen on ship specifically.
Now take a look at the tool stats. It's laser stats are very low, and none of them match up with the green upgraded laser modules. And projectile and grenade are much higher, although the relationship between the upgrades and the colours seem ambiguous.
My best guess is there is a base stat multiplier for colours, and it -might- go into negatives. If you have a -2x bonus multiplier for green upgrades to your laser, it follows that you wont see your green bar go up, and the actual ability of your laser drops.
That's my guess, at least.
edit: further, my guess is that all upgrades in your gear take effect, however you get a bonus for have adjacent upgrades, or upgrades that have some sort of relationship that give you the highlighted patterns you see. So if that's the case there are a few factors here:
1. Tools have base bonuses, these could be hidden, but my guess is they associate with an upgrade colour type (those colours I am also not entirely sure about what they represent, they may have a relationship with what sort of material you need to make it?).
2. When certain upgrades are adjacent to each other, you see these highlighted effects around the border of a particular colour. You also see bars on the right under each stat of a particular colour, and we know these bars go up and down depending on what you slot into the weapon (as per daymeeuhns post).
3. There may be negative stat bonuses, that make certain weapons/tools -worse- at certain sorts of upgrades.
If we take any/all of this to be true, then it leads me to believe that the mechanics for upgrading are pretty robust. You would want to have a default layout that is congruent with the sorts of upgrades you want, additionally, you'll want the base stats to accommodate or accentuate the upgrade types/colours you are focusing on. They seem to be able to max out, so you can't just go hard in one category, but its probably impossible to max out in all categories, thus finding the right balance will be a struggle. You can spend more money/effort probably putting things like 'beam upgrade mark 4' in a slot, and it is more powerful than a mark 1 or 2, but costs a lot more and since you can't move, it hurts more when you want to restructure your upgrade pattern.