Currently, OfficeClip does not provide hiding custom application (for which the application id  > 100). 

A workaround for the above issue, we can set the custom application number to an un-used OfficeClip application id (say: Alert application (id: 15) application), and block that application in the role application block section.

If you are adding the custom application in left bar and using Alert application (id 15), then you can add the below code in appmenus.xml inside any one of the

<Leftbar> ... </Leftbar> tags as below

<Leftbar>
...
...
<LeftbarItem appId="15"                         
               name="{Replace with your application name}"
                    url="{Replace with url you want to redirect}"
                    fontIconCss="icon-oc-document leftBarIcon"/>
...
...
</Leftbar>