Hey InterDimensionalOwl!
Cogmind can be a frustrating game for some types of players, since aside from all the core mechanics and UI info shared via the tutorial messages, context help, and manual, in terms of world exploration it doesn't hold the player's hand
at all 
So there's a lot to be discovered, and it can be overwhelming.
An example I just had earlier; I had discovered a hidden(?) door/access point/trap that was blue in colour, unlike the orange doors in the rest of the level. Unsure what it was I tried to ID/look at it, I couldn't. So I am unsure what is it, ie: door in the wall, hatch in the ground, trap, etc. Does the colour blue signify that it was a hidden door? I know I can just walk through it, but not knowing what it is break immersion and adds to the growing list of objects and concepts to work out later. I found it confusing that I can look at some terrain/object features but not others, i.e. the object in the same room I was able to ID as a 'matter filter'.
Only walls and doors are not identifiable/scannable, mainly as a necessary UI limitation (although as of Beta 1 keyboard players are now allowed to inspect them). I'm surprised you've been as far as you have and haven't seen more explicit info about them. They're hidden doors, yep, which you won't know about until you see an enemy combatant use it, or if you approach them yourself. The in-game way to learn
what those are specifically is when you, one day, use a terminal hack that reveals all of those nearby. They're called "emergency access points" and a label will pop up showing what they are. You can also equip a Structural Scanner, which reveals them on sight, also with a label naming them. If you have an Operator ally, they will also identify those and label them. There are a number of ways to figure out most things in the game using in-game methods.
My second confusion came about with a Datajack object and a trap. I found and picked up a datajack, after reading the item description stating you can use the datajack on a trap to disable it via a melee attack. Approaching a trap a few turns later I attempt to try this to no success. I check the controls page and try left clicking to attack mine, I tried force melee attack, finally I tried bumb attacking. The mine explodes and I am left a bit confused as to what I was doing wrong. The log doesn't tell me that I failed an attempt or missed an attack.
You'll have to show me your log, because I think you've missed something here. All you need is an active Datajack and to walk into the trap, which automatically attempts to disarm it. All relevant messages appear in your log. For example:
Here all I've done is have an active Datajack and click on the trap itself (or just bump into it via the regular movement keys). In this case it was reprogrammed, but since it was a low-tier basic Datajack, there was also a chance it could've exploded in my face, in which case it describes why that happened in the log. If you see absolutely no message but it triggered, the only possibility is that you deactivated your Datajack and tried to move onto it, but that's not even possible until you override the UI block and warning for moving onto a known hostile trap
The other possibility is that you didn't see there was more than one trap (they are usually found in groups), and disarmed one but then immediately ran into another.
Can the log be tweaked to show turns seperators, or colour code log entries (player, enemy, environment)? Or otherwise make it easier to determine what happened in the turns leading to my death. I often feel I don't know what is going on. In combat I seem to miss a lot and don't seem to clearly see the health of my opponents, or who hit who and what explosion trigged all the carnage.
Combat details have their own log. F8, top center console, and you can change the level of detail in the options.
Seeing the health of enemies is not as important as it is in other games you're used to, but any time they actually sustain a core injury, their new core integrity is reported directly on the map right next to them, color-coded for how damaged they are: green > yellow > orange > red.
You can also simultaneously see the general health status of all enemies in view, simultaneously, by pressing '1', or by clicking on the "[Hostile]" button in the scan window.
I would appreciate any advice or tips.
Everyone learns differently, but maybe you should read the manual? I don't suggest that new players do that because it's a lot of info, but you're not really a new player at this point and could probably benefit from reading more explicit descriptions of, for example, the optional UI features. There's a whole section on "Advanced UI" in the end which tells you all kinds of stuff
