A similar thought occurred to me when I read this article. By not making a clear distinction between innovative, true "startup" enterprises and new small businesses following established business models, it's easy to make a grave error when looking at the data. Yes, there may be fewer small businesses starting. But I think a lot of that has to do with consolidation in industries such as retail, hospitality, and food services.
Back in the 1970s, there were thousands of small, independently owned grocery and retail stores that have been pushed out by large chains. I don't fault people for preferring to buy their food and clothing from large, brightly lit, lavishly appointed and stocked stores with low prices. Personally, I wouldn't choose to buy my groceries at a rinky-dinky corner store that was common in this country forth years ago when I had the option of shopping at a modern Super Target. But that means that people aren't opening small stores and small restaurants, and small inns like they used to.
But the loss of those businesses as entrepreneurship opportunities may have drained a little bit of the color out of our country's culture, it hasn't affected our innovation engine very much. If anything, the demands that larger scale enterprises like Target and Kroger and Chipotle and Holiday Inn Express for efficiency and logistics have spurred American innovation on, and the expansion of these companies have made the average US consumer's life better by bringing them a better selection of higher-quality products and services at lower prices, increasing everyone's standard of living. (Admittedly, at the cost of a degree of homogeneity).
So we could have fewer opportunities for entrepreneurs to start successful new businesses, but still have expanding opportunity for a certain type of entrepreneur to start truly innovative companies opening up brand new markets and doing that "disruption" thing. We'd have to take a closer look, and separate out new dry cleaners and dentists offices from technological innovators.