This is a growing trend that's been really starting to annoy and frustrate me. Especially when the in-linking is masquerading as an out-link. To often there is no out-link and I'm forced to open a new tab, and "manually" search for it.
It's one thing for the NY Times to be insular, but I hope the majority of online writers / bloggers, most of whom are much smaller, appreciate that to get links and be found you need to give links and help your readers find other sites they may value.