Hey there! All the 3D models are made in Blockbench which was created for simple 3D modelling for Minecraft modding but has grown beyond that but it's perfect for low poly and low resolution 3D modelling :D
It even lets you animate inside it and export those animations for use with engines like Godot (which is how everything in Growth is animated).
It has the option to edit textures directly on the models inside the software and it's pretty good although sometimes I do edit the texture its self with Aseprite (but any other pixel editing software works fine too!) when I wanna get a little more technical :)
If you've got any more questions feel free to ask away, maybe one day I'll do a video on my modelling process for Growth :)