All-in-one software tools can be very useful, as they can consolidate multiple functions while minimizing window proliferation, etc.
For example, I recently got introduced to a nifty (albeit unfortunately named) little tool called Snowflake, which lets me have terminal windows and an SFTP file browser contained within a single window. While imperfect, I find it works better for me than using WinSCP.
Snowflake, however, is a utility. All-in-one applications in other contexts may not offer the same benefits. If you haven't already gathered it from the title, I am no longer a fan of using an all-in-one system for notes and web clips.
Capturing data is a little different than a utility in that you're accumulating data into an ever-growing bucket. And if your tool is collecting different types of data, that bucket is going to get harder and harder to navigate over time.
Yes, you can categorize and classify, but that is work. And by work, I mean time and mental effort. It then begs the question of how much time do you want to spend managing that ever-growing, ultimately unsustainable bucket of data.
I used to use Evernote for self-created notes and clippings. I thought it was great, especially the web clipper, but after years of accumulating thousands of items, I realized that all-in-one data collection was a romantic notion more than it was a practical one. In other words, I was in love with the idea, but not the execution.
This realization didn't really materialize until I spent time hunting for alternatives to Evernote. It wasn't so much that there are not good alternatives to Evernote. There are plenty of good alternatives to Evernote, such as OneNote and Joplin.
The problem is that Evernote and its ilk are simply not a good model of data collection for me. I found that mixing in my notes with clipped content in the same tool just created a mountain of data that got hard to sift through. And with that realization, I decided to separate out my note taking and web clipping requirements into two discrete applications.
For clipping, I use Wallabag, which is similar to Instapaper.
I have found this segregation of data to be very useful in terms of my daily workflow. That Wallabag will scrape URLs (it is mostly successful in its attempts) is also handy in that I don't have to worry about broken links in the distant future.
By eliminating clips from my notes, it's now much easier to find what I'm looking for, and it's been working very well for me.
Of course, I need to add the obligatory "your mileage may vary" disclaimer, but if you're finding yourself struggling with information overload because you're using an all-in-one data collection tool, maybe the best fix is to break up your solution into multiple tools.