If you check the number of backlinks shown to a top ranking page in SECockpit in a different keyword tool (e.g. Market Samurai), you'll inevitably see a different number. So, which one is the correct number?

The answer is that neither of the results are absolutely accurate. The numbers are different because they come from different indexes. The number in SECockpit comes from the MOZ index, while the numbers in Market Samurai come from the Majestic SEO index. The Majestic SEO index is bigger, but less up-to-date than the SEOmoz index. 

Ultimately, what matters is how many links Google sees and counts, but unfortunately, there's no way of knowing that, because Google don't make this information public, in any way. That's why there are services that crawl the internet and count backlinks, such as Majestic SEO, ahrefs and MOZ. Each use their own methods of finding and counting backlinks and none of them are a "perfect" simulation of Google. 

We use MOZ data in SECockpit, because they do more than just count backlinks and because we've found that in practice, their data is very reliable and has a good correlation to the real-life difficulty of ranking for various keywords.