When Brown played as a rookie in 2015, he was ONE rookie surrounded by solid, experienced veterans on the DL ... and at LB, too.
If both Shelton and Brown walk (with Trey Flowers likely leaving, too), the Pats may be relying on two or even three rookies to start on the DL. And we all saw how it went in 2017 with the lack of experienced personnel on the DL (it was a sieve) and among the LBs.
After this past season, "the Pats will be OK" feels like wishful thinking.
Your alternative - "There's always free agency" - there are a lot of DTs who haven't performed as well as Brown over the past three seasons who are already getting paid more than $7.1M. Legitimate 3-4 nose tackle types, like Shelton, are being paid pretty well, too - because there aren't really enough of them to go around.
Sure, BB has been amazing at finding underpaid/under-used "gems" on other teams, but that hasn't always worked. Neither have many of the DT draft picks that have fallen into the Pats' typical pick-range.
Declining the options on Brown and Shelton doesn't necessarily mean the Pats are "OK" with losing both of them (and, probably Flowers). If they do end up letting both walk, I'd consider the DL to be a likely weak point on the defense until we see exactly who the Pats manage to acquire as replacements. I'm not expecting that to be particularly easy. Or necessarily cheap.