Lodash is convenient, consistent, well-documented, readable, and maintainable. Yes, there's some pretty needlessly redundant methods (isNull for example), but it provides a nice API to do it. The trade-off of a few microseconds is worth it.
Omitting lodash from your entire codebase is not going to magically fix all your problems; there are much more important things you can be doing with your time, such as delivering features or eliminating technical debt.
To reduce the amount you're requiring, you can just get a specific method like require('lodash/omit'). If overhead is a concern, that helps mitigate it.
We have set it to warn, not to error; it's good to raise awareness that you're doing something that has a potential performance cost, but for things like omit the recommended native alternative just isn't worth it.
What I do find it useful for is small projects (like a lambda function) where micro-optimizations DO count.