It did get annoying to deal with the mechanics of lots of repos. So we built tooling to make that easier. For example, CLI commands like "goto analytics.js" will clone and take us to the local copy of the repo. And "publish patch" handles all the mechanics of updating History.md from the git log, incrementing the version appropriately in package.json and component.json, tagging the commit and releasing to github and npm. Khaos, also mentioned in Sperandio's article, helps us template out new repos quickly. With a few pieces of tooling like that you can move pretty fast across lots of repos.
There's also an interesting balance for things that technically should be their own repository, but shouldn't for workflow reasons since it actually means they will be more quality if they are grouped and updated at the same time. Where splitting things out can actually discourage updating if the cost is too high.
There's also a big open question around what should be a separate repository, and what is separation just for separation's sake? A similar kind of question that has to be answered for individual functions in a codebase. We've made the wrong call sometimes and split things out that should have really been together.
I tend to think that the drawbacks are worth it, since it means things are actually decoupled and generally more parts of the codebase are able to get to a "finished" state. Lots of the modules we've built haven't been touched in months or years now since they do exactly what they need to do without any bugs now.
In general I think that in programming we talk a lot about building things that are decoupled and simple, but we haven't invested anywhere near enough in tooling to quell the drawbacks to things being more spread out. The pros are extremely valuable, and the cons are solvable, we just haven't done anything about it.
Rather than go to highlightjs's website to download a custom build of the script that doesn't have 22 languages (20 of which you probably don't need), adding it to your asset pipeline, then repeating whenever you need to add a new one, with highlight's plugin approach + a simple package manager and build process like duo, you can easily add and remove each language from your build ad hoc.