Bundling to me is such a sledgehammer solution. Yeah, it can somewhat prevent many of those issues, but it also comes at a pretty large cost.
* it leads to code duplication
* it can ruin the performance of tree-shaking and minification systems
* it prevents you from swapping out a small module with another globally
* it makes it harder to inspect and debug the code that you have installed in the node_modules directory
* it makes it harder to verify that the code on your machine is the same as the source code
* the bundler can introduce bugs into the source code
* The package now needs to maintain a build step and needs to maintain a separate source and "binary"
And more. Plus, in the end you might not even be helping anything. A big repo like lodash can have just as many contributors as tons of little dependencies, and big repos aren't immune to the org running it going belly up.
I guess I see those problems as more of a "large amount of code" problem instead of a "large amount of dependencies" problem.