JMP files simply don't exist in the 'release' version of the Pikmin filesystem. The developers of the game were kind enough to leave their developer tools in the disc, containing promising .dll files, but a lot of the formats are long since gone. One of these include the .jmp file. The only reason we know of its existence is because of the dll: filterJmp.dll. Now, you may think that we cannot surely know whats inside of a .jmp file, right? Well you are semi-correct as we can use a tool called IDA that can re-assemble parts of the code. After becoming familliar with the Pikmin filesystem and how the executable files (.dll and .exe) handle things. I have made an educated guess upon what they are.
J3D Model Preset
A theory I have recently came up with is that the name actually stands for: 'J3D Model preset'. J3D being the toolkit used to create games like Pikmin 2 and Super Mario Sunshine later on in the GameCube's development. Model preset because looking at the code, it was a plaintext format that contained not only collision information, but polygonal information as well as some other unknown variables.
I have uploaded a video where, in real time, you can see me pick apart filterJmp.dll and comment on what things mean and what I'm thinking. This format is EXTREMELY UNKNOWN FROM EVERYWHERE and we cannot know anything CERTAIN about this format other than make assumptions based on the information we are given. Video is here: https://www.youtube.com/watch?v=s25T3slqZzg&feature=youtu.be