If you're talking about the walls (highlighted in red) that separate the six different chambers in the OEM exhaust, then no, they don't remove them. Those walls are also structural parts of the exhaust system.
Chambers 1 and 2 (the Helmholtz resonators) are never altered in the OEM mod.
ACM does their work inside chambers 3 and 4 only. Subw00er's "Bates valvetronic" flapper mod used these chambers as well.
Periokid and most of the early OEM exhaust modders did their work in chambers 5 and 6.
Either way, OEM exhaust mod does not equal straight pipe only.