Pixel shaders in a 2D game are mainly useful when you want some special effects rather than just displaying a plain old texture.
WADE's API for pixel shaders was designed to make it quick and easy to write simple shaders that you want to apply to your sprites. It's pretty cool if you do it from the editor because you can see what happens literally as you type, and that saves you a lot of time.
The fact that we abstract away some of the complexity (e.g. you don't have to define your shader function, you just type the shader code that you want to execute) allows us to do some clever optimizations.
If you do things manually, i.e. you override a Sprite's draw function with your own and do all the low-level stuff such as sending uniform data to the GPU and all that, you have to be a bit careful with potential performance issues.
If you let WADE handle things, it will introduce its own caching mechanism for shaders, textures and context states, so it doesn't do any expensive operations if it doesn't need to. For example, if you're drawing 2 sprites that use the same texture with the same shader, it can recognize that and save time by not associating the texture with the sampler twice. It's also got an efficient hashing system for the shader source code, so it can recognize that two shaders are the same even if you try to create them twice using the same source code, and it can do that without any costly string comparisons.
In the near future (hopefully version 3.3) there will be some more advanced optimizations that reduce the number of draw calls automatically where possible, without you, as a user, having to do anything.
If you do things manually, you don't have any restrictions whatsoever, but you lose those benefits. So my advice would be to only override a Sprite's draw function with your own when there is a very valid reason for doing so. Drawing 3D objects with your own vertex / fragment pipeline may be a good reason.
Now for best practices, I normally refer to this article for the general ideas, but its numbers are a bit outdated and you may want to look at WebGL Stats to get more current ones.
Finally I'd also recommend a quick read of mozilla's recommended best practices in case you want to do some low-level graphics programming.