The Meaning of Life, the Universe, and Everything.
I've almost never heard anyone use the 3D Anaglyph option in minecraft. Mostly because it Isn't even correctly calibrated to the correct red color.
They probably thought that so few people used it that it was basically obsolete and a waste of code. It seems like Mojang is trying to streamline Minecraft a lot, and this is just one of the things they thought they didn't need.
I tried the Anaglyph 3D mode in the game once and it was okay, but not great.
If you want a really good 3D experience in Minecraft you have to go with VR. ViveCraft works well with both the Oculus Rift and the HTC Vive on the Java Edition of Minecraft. For the Windows 10 Bedrock version VR is natively supported for the Oculus Rift, and I believe the HTC Vive as well. There is also the Gear VR version for Samsung phones with the Gear VR headset.
Yeah, these are expensive solutions, but well worth saving up for if you want an excellent 3D experience in not only Minecraft but other games as well.
I don't think anyone from Mojang actually reads these forums, so if you want to discuss this with them then I would suggest that you join the official Minecraft Discord channel and ask there as to why it was removed and what the possibility of getting it back would be.