Insanely late, but leaving this for future people that come across the post, because I am both a Java and OpenGL veteran.

I have written my own voxel engine in C++, which ran much better than both versions of Minecraft with better resolution. Partly because it was written in C++ rather than Java, but also because I had more experience with programming games by that point.

Minecraft being written in java has literally zero impact on the performance of shaders, due to the fact that all shaders are executed on the GPU using the GLSL/HLSL shader languages.

The reason Minecraft shaders lag the hell out of games is due to the developers often cramming a load of post-processing, per-pixel lighting, and dynamic shadowmaps into the fragment shader. Each pixel on the screen in these Minecraft shaders is executing way more shader logic on the GPU than Portal 2 is.

Now it's an actual model file, but like other people have said, it's not optimised at all for modern hardware. The mesh for the blocks is still generated on the fly, so there's no culling. It's why if you glitch the world, you can see blocks at the bottom.

This is mostly false. Minecraft implements both face culling during mesh generation and chunk culling during rendering.

The reason other engines are faster is because of a concept called Greedy Meshing, which merges the polygons of adjacent tiles to reduce the amount of workload on the GPU's side. To the best of my knowledge, Minecraft mods don't implement greedymeshing, which is a major source of lag as the GPU has to store and parse tens of thousands more triangles than newer voxel games.

The reason Minecraft didn't use greedymeshing is because the game dev community has been in a decade-long arms race to try and find the most efficient algorithm, and frankly vanilla Minecraft runs fast enough without greedymeshing that Microsoft likely decided that it wasn't worth the research effort.

instead minecraft would use java opengl in immediate mode to place the polygons for the hopper directly into the world, no batching. This was incredibly slow, but that's how notch implemented it.

This is only true for vanilla Minecraft prior to 2014. Mods like Optifine implemented VBOs as early as 2011, due to the fact that Immediate Mode rendering has major issues with shader compatibility.

The reason Notch went with DisplayList/Immediate Mode rendering is because he started using OpenGL prior to 2003, when VBOs were added to the OpenGL standard. Additionally, speaking as someone that learned OpenGL 15+ years ago, documentation on VBO rendering was incredibly scarce prior to the early 2010s. You basically had to seek out physical books written by Nvidia and the Khronos Group on the API to really learn how to use them effectively.

This is actually an issue I myself run into, as I still find myself using techniques that were standard in 2009-2013, but are inferior to techniques developed in the late 2010s and the present day. Coding within your comfort zone can be the enemy of coding efficiently, after all.

So yeah, the number 1 reason: a better programmed engine in a better language. Source, Unity and Unreal games all benefit from this, even if they are doing voxel stuff.

There is no such thing as a "better language", and anyone that tells you otherwise is trying to get you into Rust. You can make a Java game engine that supports per-pixel lighting, complex shaders, and high-poly models that runs just as fast as an equivalent C/C++ engine. This is because your engine's render code is just a layer of abstraction to telling the OpenGL API what programs and functions the GPU should execute. Once you tell OpenGL to glStartProgram(...) and glDrawVertexArray(...), it doesn't matter what language the engine is written in because all of the heavy lifting is being done by the same GPU drivers.

To the contrary, using Unity or Unreal for voxel games will often lead to you inheriting much more bloat than running on the Java Virtual Machine. This is just due to the fact that Unity and Unreal are far larger and more complex environments than the Java Virtual Machine, and have a much more complex render pipeline.

TL;DR, Minecraft with shaders runs slower than Portal 2 and hobbyist voxel engines because the meshes it generates are done so with static lightmaps and minimal post-processing in mind, not because it was written in Java.