Accessing an iso from a hard drive is far, far faster than using the Wii's DVD drive. You're likely experiencing shadercache issues. The first time any effect is used for a given object, Dolphin needs to design and compile a shader that will have the same effect. After this, it can use the shader it's already made, so as long as you stick to one Dolphin build, you'll find this stops happening as much as you progress through the game.
OS: Windows 10 64 bit Professional
CPU: AMD Ryzen 5900X
RAM: 16GB
GPU: Radeon Vega 56
CPU: AMD Ryzen 5900X
RAM: 16GB
GPU: Radeon Vega 56
