Thanks @anoori for raising this. There are two major flavors of ImageJ: ImageJ1 and ImageJ2. They have different logos.
The original version of ImageJ, still developed by Wayne Rasband. There are no plans to change or update this logo.
The version of ImageJ funded in 2009 by NIH to redesign it with expanded capabilities. Features a backwards compatibility layer to ImageJ1, and a new data model backed by the ImgLib2 library.
Note that the logo of ImageJ2 above is new (designed by @imagejan and colorized by @elevans). We had a community logo redesign contest, and this logo was the winner. We are on the cusp of launching a new ImageJ wiki to replace the old one (preview here), which will switch over to the new logo across the board. We also still need to update the ImageJ application to use the new logo, but that is coming as well.
The Fiji distribution of ImageJ (spelled “Fiji”, not “FIJI”) is built on ImageJ2. Fiji predates the development of ImageJ2, and thus was originally built on ImageJ1, so it got its own logo at that time. There are no plans to change or update this logo.
For Simple Icons, I would advise adding the new ImageJ2 logo, as well as the Fiji logo. I’ll respond as well on the GitHub issue, including replying to some of the specific discussion points there.