The 'Gateways' series came out in 2001, so I'm not to sure what interconnectivoty you are referring to, aside from possible 'Invasion' in 96. The Section 31 mini-series from 2001 was thematically linked, with the only book that had impact on any others being the DS9 entry, as it was released as #3 in the relaunch, but the TOS, TNG & Voyager entries were seperate; TNG's entry took place shortly before Star Trek First Contact and did introduce Ranul Keru.
"Double Helix" was also thematically linked, as books 1-5 took place between 2364 and 2375, while book 6 was in the 2330's to 2350's timeframe.
Again "Day Of Honor" was thematically linked with Worf appearing in 3 of the books.