Make use of sample indexes and samples table more consistent

[stuzart]

Currently a bit mixed, using indexes on some pages and for sample types and templates using the samples table. Data file samples were also shown as a table, but fixed as part of #2052 to show extracted samples only in a table (due to mixed sample types for related_samples).

For sample types and templates, samples are shown in the related items tab, with a link that is expected to go to the standard index and filter page, but takes you to the table instead.

Suggestion is to always show the standard index and filter page for sample lists, but where there is a single sample type selected, give the option to view in the sample table view. Also refactor the sample table view to be a bit clearer and more consistent on how it is used, and ensure only visible samples are shown.