pruning make no sense

“pruning make no sense” means pruning has no effect on plants?

I assume you mean ‘pruning makes no sense’? It doesn’t necessarily mean that it has no effect, it simply means that it’s illogical to do so :)!

To add to the above:
‘pruning’ can also apply to nouns other than plants. Any trimming and removal of superfluous (unwanted) parts could be said to be pruned.
For example, a piece of writing might be pruned if it is considered to be over-long and contain unnecessary text.