Show all gaps: Nothing is hidden.
Show some gaps: For each column range (consisting of gaps only) a different amount of gaps is shown, depending on the width of that column range. In detail:
sequence has less than gaps => display that many gaps
Hide all gaps:
Hide no nucleotides: All column ranges consisting of gaps only are hidden.
Hide columns with less than X% nucleotides: This mode really makes nucleotides disappear from display. Use with care!
Those above mentioned column values are calculated on the basis of all sequences currently loaded in the editor.
Only sequence data is taken into respect while calculating gap positions. It is possible, that parts of a SAI get hidden by using OSC.
You may use <CTRL-K> to toggle between 'Show all gaps' and 'Hide all gaps' while the focus is inside the sequence view.