There is no design that is better for SEO - there are rules for content, the only way a single page app could rank higher than a multi-page app is by the content you are showing off. Basically, one of the most basic rules would be to have more than 15% relevant text content on a page. In most multi-page apps this is not possible and because of that, a single-page app that doesn't follow all the rules can sometimes rank higher.
Regardless of this single rule, there are many techniques that you can use to rank a site high, with another example being backlinks. It is logically understandable that a single page app will only have backlinks to its index whilst a multi-page app can have them divided.
It would be better if you provide some examples and test them with various tools like pagespeed, yslow, woorank, etc to have a general understanding of how those sites work in "trending" SEO. Even so, these tools will not total all the algorithms used by search engines and without having access to trending search engines webmaster tools, you are unable to know all the gimmicks a site uses to rank high. For example, even if a site is single page, the sitemap can divide itself into all the links available in the navigation, providing custom content crawlable by search engines. A complete SEO analysis of the sites you are looking at will give you better insight than any answer given here, as research is always better than guessing!
Keep in mind that every search engine has some basic rules and you really need to dig into these sites a bit to figure out what you are dealing with.