If you want to hide custom columns in wiki page, you can edit this file C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\DocumentTemplates\wkpstd.aspx. It's the template of wiki page.
You can comment this entire section, which renders additional column list. Or you can add your column name, which you want to hide, to ExcludeFields property
<TABLE class="ms-formtable" border=0 cellpadding=0 id="formTbl" cellspacing=0 width=100%>
<SharePoint:ListFieldIterator
ControlMode="Display"
TemplateName="WideFieldListIterator"
ExcludeFields="FileLeafRef;#WikiField"
runat="server"/>
</TABLE>
You can find more about ListFieldIterator here http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.webcontrols.listfielditerator.aspx