So, there isn't a hard distinction made between earlier books and current ones, it's more that after the TV shows started ending, the books had a wider set of possibilities to play in, and as the narrative became more serialized more authors kept - by choice - attaching their stories, until a pretty enormous interconnected continuity resulted.
It wasn't planned that way, or rather it wasn't all planned that way, but it kept being more fun for authors and readers when the stories connected. The flowchart makes no judgement as to quality - there are a lot of great novels not on there - those are just the books that inter-relate the most. Thankfully, the vast majority of the interconnected stores are
remarkably great novels, on average I'd say vastly above the quality of the numbered novels.
If you love DS9, the place to start is the DS9 relaunch. Ignore basically everything that connects to it except possibly Mirror Universe if you're into that. The first 5 stories are collected in an omnibus titled Twist of Faith. That omnibus includes DS9 entries into two crossover miniseries - Section 31 and Gateways - but you really
don't need (or probably want) to read the other entries in those miniseries. So when that all crosses over on the flowchart, don't let that scare you off. Just read from Avatar straight down to The Soul Key, and you'll have a blast
After that, the usual recommendation is to skip the first 6 A Time To... novels (which ended up being pretty minor works) and start the big interconnected middle section with A Time To Kill. From there, read everything in the TNG / crossover / Titan columns below that. That's the heart of the ongoing continuity, especially the Destiny and Typhon Pact stories. (And Voyager, starting with Full Circle, is also incredibly good, perhaps the best novel series currently running. That comes from someone who didn't like the Voyager show at all; when/if you get there, you should really give it a shot. One winner after another.)
Alternately, since you say you're a TOS fan, if you're looking for a smaller time investment the Vanguard series takes place during TOS on a space station, and is just goddamn made of awesome
. It's only 8 books and it's over, ended on purpose, and there's definitely something appealing about that.