SHUNT'S Blog explains a nice way to disable shuttle items.
I changed the javascript a bit to support Apex 5.0, and added a background-color css style for the disabled items.

Source: http://simonhunt.blogspot.nl/2012/11/disable-shuttle-item-values.html

Page

Identification
	Page ID	1088
	Name	Apex - Shuttles - Disable Shuttle Items
Javascript
	Function and Global Variable Declaration	function shuttleMove(pMove1,pMove2) { $("#P1088_SHUTTLE_1_"+pMove2+" option").each(function () { if (!$(this).attr('disabled')) { $(this).appendTo('#P1088_SHUTTLE_1_'+pMove1); } }); }
	Execute when Page Loads	var valDis = ':' + $v(P1088_SHUTTLE_1_DISABLED_ITEMS) + ':'; $("#P1088_SHUTTLE_1 option").each(function () { var valThis = ':' +$(this).val() + ':'; if (valDis.indexOf(valThis) > -1) { $(this).attr('disabled','disabled'); $(this).attr('style','background-color:#CCCCCC;'); } }); $('#P1088_SHUTTLE_1_MOVE_ALL').replaceWith('<a onclick="shuttleMove(\'RIGHT\',\'LEFT\');"><button id="P1088_SHUTTLE_1_MOVE_ALL" class="a-Button a-Button--noLabel a-Button--withIcon a-Button--small a-Button--noUI a-Button--shuttle" type="button" title="Move All" aria-label="Move All"> <span class="a-Icon icon-shuttle-move-all" aria-hidden="true"></span></button></a>'); $('#P1088_SHUTTLE_1_REMOVE_ALL').replaceWith('<a onclick="shuttleMove(\'LEFT\',\'RIGHT\');"><button id="P1088_SHUTTLE_1_REMOVE_ALL" class="a-Button a-Button--noLabel a-Button--withIcon a-Button--small a-Button--noUI a-Button--shuttle" type="button" title="Remove All" aria-label="Remove All"> <span class="a-Icon icon-shuttle-remove-all" aria-hidden="true"></span></button></a>')

Item

Identification
	Sequence	10
	Name	P1088_SHUTTLE_1_DISABLED_ITEMS
	Display As	Hidden
User Interface
	Region	Disable Shuttle Items
List Of Values
	Display Extra Values	Yes
	Display Null Value	No
Advanced
	Warn on Unsaved Changes	Page Default
Source
	Source Used	Only when current value in session state is null
	Source Type	Static Assignment (value equals source attribute)
	Source value or expression	CLARK:FORD:KING:SCOTT:JONES

Item

Identification
	Sequence	20
	Name	P1088_SHUTTLE_1
	Display As	Shuttle
User Interface
	Region	Disable Shuttle Items
List Of Values
	Display Extra Values	Yes
	Display Null Value	No
	List of values definition	select ename as d , ename as r from emp order by 1
Advanced
	Warn on Unsaved Changes	Page Default
Source
	Source Used	Only when current value in session state is null
	Source Type	Static Assignment (value equals source attribute)
	Source value or expression	ADAMS:JONES:MILLER