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Many times colors go with branding, in most cases it wouldn't be possible to change the color according to the user's time.

You could put a switch to enable "night mode" for your website, but if your visitor knows about this problem he'll already have either f.lux installed, or native options enabled.

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Yep. And although my own work leaves me with complete creative freedom (I do all the branding), I am looking at Facebook and thinking that the small blue bar at the top is probably subtle enough to not have a big effect on the eyes. Certainly not vs. my site (https://suitocracy.com) which has... uhh, a bit more blue than that.

Looks good.

I don't think that shade of blue is that bad for your eyes. I for instance have a gradient between fuchsia and purple, and it's probably worse.

The problem is not blue parts of the picture, but overall level of blue light, which is coming mostly from white parts of webpages. In particular, the dark blue parts of your page have the blue channel at less than 1/10 as intense as the blue channel in the white parts of your page (remember, the sRGB values are gamma-adjusted).

It’s better to make your design look good (I recommend lots of lightness contrast especially for text, and nothing too outrageously colorful), and leave minimizing blue light exposure to the user/browser/OS.

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