Dear Ivan,
The main reason for deprecating these functions was probably that none of the 330 packages in CVS uses these functions, tcllib contains a more complete collection of functions (package req struct::set, see [1]) and maybe to provoke feedback like this one :)
I would recommend to use struct::set, which is the standard tcl-way; another option would be to make an own package "setutils", having these functions non-deprecated. The probably most efficient counterpart for set_member is the "in" expression (e.g. "if {$x in $set} ...").
all the best
-g
[1] http://docs.activestate.com/activetcl/8.5/tcllib/struct/struct_set.html