I think the zoom level consideration is one of those technical factors that's largely out of your (and Alex's, for that matter, given how he's rendering) control; different GPUs will handle the fine details of rasterization at different zooms differently.
About the only way to get semi-firm control over that would be to render the sprites with a shader pass designed to arrive at a very specific outcome, in terms of what people will see. It's quite possible to run a shader to do pixel-pixel comparisons, sharpen up heights, etc., although once again, you get into some compromises, such as having to be quite careful about adjacent pixel values for some things, using some very specific colors as control objects, etc.
So there's a lot of that that's kind of beyond your control as an artist. the main issues are, to my mind: "does it look really hot at 1:1, in the equip screen" and "does it look terrible at max zoom on our test hardware because <insert thing here> is problematic as pixels get averaged".
If neither is an issue, it's working about as well as it's going to. With shaders filtering the results to a very specific requirement (i.e., rendering out all ships, weapons, etc., to a FBO first, then manipulating, then writing a quad to the screen), you can tune things better.
Here, we're looking at what could happen with different filters, at 2X zoom. This is bicubic, bilinear, nearest neighbor, bicubic_smoother + nearest neighbor @ 50%, bilinear + nearest neighbor @ 50%. This is further out than Vanilla lets us zoom out, of course, but you can see a lot of difference, in terms of quality and feel. Most GPUs are basically doing bilinear passes, but aniso steps in to re-sharpen a bit, if enabled, so it's a good starting place but suffers from a bit of mush. With a shader, you can control it a bit better across hardware.
A shader could even do a bit of rebalancing after that filter is done, adjusting contrasts a bit, like using Curves, resulting in better overall recognizable shapes and such, too. Bilinear, with enhancement (a Curves step, basically just a push filter, followed by a Sharpen step, which is a nearest-neighbor filter):
And that could happen in a really subtle way, based on a zoom value sent to the shader as a uniform, so that it doesn't pop from one thing to the other.
Anyhow, there is a lot of stuff that's possible there, at a technical level; shaders to do post is probably the best single tool besides what's in the art. I agree that what's in the art can make or break the piece, but I think there are things that can be done to minimize the impact