Indexation usually refers to the status or health of a site's currently indexed pages in a search engine. One of the primary goals of SEO is to get every page on the site, or all of the most important pages on the site indexed by the major search engines. A site's indexation refers to the status or progress of this process. The word "indexation" can also refer to the actual process of adding pages to the index.
If a high percentage of pages on a site are indexed, the site is said to have "high" or "good" indexation. Likewise, if a low percentage of pages on your site are indexed, the site is said to have "low" or "poor" indexation.
There are many factors that contribute to the overall indexation of a site. Below are some examples:
Internal linking strategy
Site structure and depth
Number of external links to the domain
Number of external links to each page
Deep links into the site
Authority or trust of the domain
Size of the site
Presence or absence of redirection problems, 4xx or 5xx errors
Presence or absence of duplicate content
Frequency of site updates