I'd call them "non-icons": they don't communicate in any way, they don't add significance or separate one application from the other at first glance, they don't really mean anything without the file name, they are really not much better than default icons. And this is probably what they are: default icons for a group of applications with a bit of variation sprinkled on top.

At this point, does it need that residual variation or is this just adding noise? Also, a shape inside a shape inside a shape inside a shape isn't anything anyone is likely to parse – how many bits of information is this? So maybe just go with a simple default wrench icon for all of them?

PS, Another way to put this: are these still icons, as in "indicative of something", or are they merely ornamental, particularly in their individuality? And, if the latter, how good are they as ornaments? Is there even a need or a place for ornaments in an interactive environment that is meant to be tuned for efficiency?

(In my experience, if an interface elements raises questions, even more so, if these are fundamental questions, you do have a problem. If not for other reasons, just for the few more bits of awareness spent on these questions, every time you see them.)

Indeed, all you can do is learn and memorise what they represent. But a square filled with a solid color can do the same ("yellow is the hard disk thingy"), and that would actually be more glanceable and quicker to distinguish.

If your icon loses to a yellow cube, it is not a good icon.