I've checked your demo with both the latest version and the last stable version (188.8.131.52) and the behavior is identical, i.e. <Hidden Columns> has no effect on Filter rows.
Using trace on browser refresh, I found that this is caused by the order in which the display is initialized, where the <Hidden Columns> element is set before the filter group is initialized (by Hide Column Demo/View 2/TestTBL/Init/Init Table Header by Configuration).
To resolve this you should make sure that <Hidden Columns> is manipulated only after the filter group is initialized.
For best results, use the Firefox browser..