I am currently making clouds and I was wondering if I could be efficient and make one cloud and let the computer randomly choose where it could make it transparent or do I have to make multiple meshes?
Create a texture (like clouds, voronoi or musgrave or even an image texture) and have that texture control the mixture between the base cloud shader and a transparent one. Additionally, you can use a color ramp to control the contrast on the texture.
A more computationally intensive approach to making clouds, would be to use a texture to control the density of a volume scatter shader connected to the volume socket of the material.
To make random parts of your mesh transparent, you can go to edit mode, then click the button on the bottom left of the 3D Viewport labeled "Select". Then click random to select a random number of vertices, edit the amount of selected vertices in the left side window. Create a vertex group from this selection. Add a mask modifier to the object targeting the vertex group you created.
This however, is not a very good way for making clouds.