First wave small brands Makaha and Hobie only sold product until skateboarding's second death. Makaha intermittently resurfaces as Poweredge, while Hobie continues to make surf and sailing equipment.
Sims, Walker, and Logan Earth Ski were the first wave of skater-owned small brands that, to some degree, still exist. When those and other surf companies got bigger, a wave of former pros branched off to create their own small brands: Powell Peralta, Alva, Dogtown, Z-Flex, etc. They have all been relevant and have had long lifespans.
The cycle of small brands becoming big brands and people starting their own small companies have continued: SMA, Madrid, Skull Skates, Zorlac, Blockhead, Uncle Wiggley, Schmitt Stix, SMA/Rocco, H-Street, World Industries, Shut, New Deal, Alien Workshop, Real, Birdhouse, Girl, Foundation, Deathbox, Consolidated, Think, Zoo York, etc. Many of those brands owned their own woodshops, hired their own staff, and used their own distribution channels, which I believe describes the intent of the original post (Life, Plan B, Focus, Mad Circle, Menace, Chocolate, Toy Machine, etc. either attached themselves to existing umbrella companies or were expansion teams).
TL;DR: The waxing and waning of small skate brands, until Nike came along, has been the business model for the skateboard industry.