They will be treated as raw coins, since NGC only crosses PCGS coins. Whether there is any benefit in leaving them in the slab is a matter of opinion. Some think it gives the submitter an advantage, others feel the opposite.

I have submitted a few ANACS coins in the original slabs.  Most have graded a point lower at NGC - an ANACS MS-64 came back NGC MS-63, and three 65s came back 64s.  A couple came back with the same grade, and one jumped up from VF-30 to XF-45. None have come back details graded so far.  I have never cracked one out for submittal.  

I have submitted both ways to NGC and my experience has always been a lower grade and often times a return as not eligible for crossover when they are still in the holder. I have had better luck cracking them out and sending in as a raw coin. The grade outcome is about the same meaning they always come back from NGC with a lower grade, sometimes very disappointing outcome. I do it because my personal preference is true grades from NGC. Since I always buy the coin and not the holder I accept the grade given by NGC.  

thank you all for your feedback

It might depend on the kind of coin.

They seem to be under grading old Islamic gold.  I have cracked out several dinars from ANACS holders and sent in as raw to NGC and they always come back higher, sometimes by a lot.

I pasted some ANACS to NGC ones I've had come back.  I always just broke them out and sent as raw.  

Crack them out and send them in.

I've submitted several coins in their ANACS holders. All have crossed at the same grade or one grade higher.