Hmm. I do see what you mean. I checked a file of mine that has a lot of Layer Groups, and the disabled lock icons have a similar grey-ish color. I think I may have missed editing them when I designed the theme modification (or are they colored Disabled using code?)
But here’s the thing though, I’ve been using this modified theme for a few months now, and I honestly haven’t had any confusion, and didn’t even notice the grey-ish colored disabled locks in Layer Groups. So ultimately, even if a design is “inconsistent” what is more important is that it is “human sensible.”
For example, when Apple Made Their Shuffle Feature Less Random, to Make It More Random. Sometimes hard-logical True Random “feels repetitive” – because if a song repeats 6 times in a row, technically that is still “random” from a mathematical perspective, but to our odd human perspective it feels “wrong” and “not random.”
And so at some point a change was made so that when you now press shuffle, the list of tracks is reorganized into a new list to played one by one. That prevents the same track coming up repeatedly. It is less random, but it feels more random to users.
So Apple fixed a problem that was “technically correct” but still “felt wrong” to users. I think this Aseprite lock icon is one of those situations.
Yeah you’re right that the grey lock does “look disabled” on first appearance – but from my experience actually using this theme daily, for the past couple months, it hasn’t caused me any confusion thus far. It’s still much more readable, and it “feels right” when using it daily, and it saves me mental energy trying to figure out what the icons mean. And I’ve shared it with a few friends, and they also said it was an improvement.
The current icons both look like black blobs to me at a distance of more than a foot or so. One of the best things my high school art teacher taught me was the “squint test” – that any art piece should be fully readable when you squint your vision until it blurs, and nothing but the vague shapes appear. Here’s an example of the current Aseprite icons versus my modification:
(I used Aseprite’s Blur x9 filter to simulate squinting)
In the Default theme, you notice, the “eye” icon is very readable (you can still tell when it’s closed or open). The “continuous cels” icons are very readable (you can easily tell which is two dots, a long line, or a folder, even with very bad vision!). But the Lock icons are all black blobs. You can kind of tell which is unlocked, but you have to focus and really examine each icon. My sample on the right is instantly readable.
With my Theme, if I squint my eyes or look at my monitor from 6 feet away, the “black” lock icons represent locked, and the “not-black” ones are “not-locked” – it’s very readable and sensible, even from across a room at a glance – or for anyone who has visual impairment (near sighted like me).
Looking at another art program I use, Clip Paint Studio, this is what they do as well:
The “Eye” and “Lock” icons don’t have alternate frames – they are simply removed when not toggled, making the GUI very readable. There is no “unlock” icon, just “lock exists” or “lock doesn’t exist.” Same with the eye.
I think this is just the only real sensible way to do it. Its how other programs do it, because it works and is consistent with how human brains work.
To sort of demonstrate why this is such an issue for me personally, here’s a photo of my workspace:
This is me sitting about 2 feet from the display, with my hand directly pressed against the screen. I have a small portable tablet screen with 1080p resolution, and very High DPI display. So the pixels are incredibly small. In comparison to my fingers, or my pen, the icons are tiny. But the issue isn’t UI scale – this scale is actually very good for my workflow (my scaling is set at 200%), the only icons I have issue with reading are the lock icons, really.
Even if you squint at the Tools or other menus, they are still very readable!
You can tell exactly what each icon is, even with blurred vision. Very good design, very distinct.
I honestly love the GUI on Aseprite – its so good, and my favorite program to work with. It literally is only the lock icons I struggle with, haha. So I don’t want to give the impression that I’m upset or complaining, or anything like that. 
But now that you’ve mentioned the similar “disabled” icons, I might experiment with modifying my theme too. Even though it hasn’t caused me any confusion thus far.
Perhaps the “disabled” icons could have an X over them, in some fashion? Or maybe “disabled” icons could have some sort of symbol/icon that represents “the group this layer is in, is locked!” Not sure. But I’ll play around with it and see what I can come up with.
this is a good idea, not sure about the icons yet (the gray icon is already used when a group is locked, so children layer are displayed with a grayed icon).
