Are you cleared to next altitude when you get "direct" while flying SID?
As an example, say you receive an IFR clearance from clearance delivery prior to departure such as: "N1234 cleared to Los Angeles Airport, ATOME TWO DEPARTURE, ARRIE Transition, Q-One Forty-five, climb via SID, Squawk 2252, etc." Then, after passing 2000 ft. if the tower controller instructs you to "proceed direct ZUMBI" then he/she (controller) should issue you an altitude assignment because you are being taken off of the lateral path of the SID.  In the alternative the controller could assign an altitude by using the phraseology (or similar) "N1234 proceed direct to ZUMBI, climb via the ATOME TWO departure." The "climb via" verbiage in this sequence is the equivalent of assigning an altitude. 

After switching frequencies to the radar controller he/she should instruct you (for example) "after ZUMBI climb via SID" (assuming that ATC wants you to meet the KIMSH restriction and climb to the published Top Altitude of 15000 ft).

Here is some information from the ATC Controller's Handbook 7110.65W, para. 2-6-4, g. 2 and the associated Note: (Air Traffic Controller's handbook, 7110.65W)

(Although the reference paragraph and note, as it is published in the controller's handbook, is an example when a deviation around weather is necessary, the principle underlying my explanation is the same (there is just not an example similar to the circumstances you describe in your question).


  
  When approving a weather deviation for an
  aircraft that had previously been issued a crossing
  altitude, including Climb Via or Descend Via
  clearances, issue an altitude to maintain along with
  the clearance to deviate. If you intend on clearing the
  aircraft to resume the procedure, advise the pilot.
  
  
  NOTE−
  
  After a Climb Via or Descend Via clearance has been
  issued, a vector/deviation off of a SID/STAR cancels the
  altitude restrictions on the procedure. The aircraft’s Flight
  Management System (FMS) may be unable to process
  crossing altitude restrictions once the aircraft leaves the
  SID/STAR lateral path. Without an assigned altitude, the
  aircraft’s FMS may revert to leveling off at the altitude set
  by the pilot, which may be the SID/STAR’s published top or
  bottom altitude.


Also, from the FAA's Pilot/Controllers Procedures &amp; Systems Integration Workgroup FAQs regarding "Climb Via" procedures, here is an applicable Question and Answer (FAQs Climb Via):


  
  Q. 
  I’m on a climb via clearance and the controller vectors me off the procedure.  Do I continue to “Climb Via?”
  
  A.  NO.  You are laterally and vertically off of the
  procedure.  The controller will issue an altitude to 
  maintain and provide a further “expect” clearance.
  Note: Request an altitude to maintain if the 
  controller does not provide one
  


The main point is that a clearance to fly a SID that contains a Top Altitude and verbiage that includes "Climb Via" assumes that you will fly the lateral route as published, thereby committing you to meet the altitude restrictions.  If you are taken off of the published lateral routing ("cleared direct" to a fix somewhere down-range on the SID) the controller needs to issue you an altitude assignment since you (while proceeding direct to ZUMBI) are no longer on the published SID lateral route. In the alternative the controller could assign an altitude by using the phraseology (or similar) "N1234 proceed direct to ZUMBI, climb via the ATOME TWO departure." The "climb via" verbiage in this sequence is the equivalent of assigning an altitude.

From the NBAA Access Committee briefing regarding "Climb Via" procedures:
(NBAA Climb Via Briefing) showing ATC Phraseology when being cleared direct to a fix on the SID.



Pictorial display from the NBAA briefing (see link above) of pilot/controller responsibilities and phraseology when being cleared direct to a (down-range) fix on the SID after departure: 



If the controller did not issue me an altitude instruction ("maintain," "climb via," etc.) upon taking me off of the SID I would have asked for one.

Here is a link to the ATC Controller's Handbook (7110.65W) so you can review the reference noted above. Also, here is a link to a FAQ's publication regarding Climb Via Climb Via FAQs