I am not sure what your intended purpose is for these coverslips.  If you are trying to make the hydrogel stick to the slide you will need some sort of immobilization chemistry.  Generally if the slip is hydrophobic, the hydrogel will delaminate from the slide once it is hydrated.  If you are trying to get the hydrogel to come off the slip, this may be a good approach.  Simply putting the slide in NaOH will help clean the slide as it should help to remove organic material; however, this wouldn't make it more hydrophobic.  If anything you may oxidize the surface and make it hydrophilic.  If you want to make it hydrophobic, clean it with the slide (NaOH is fine although other methods work), functionalize the surface with -OH groups (with a plasma cleaner), and then you can use something like octadecyltrichlorosilane (OTS).  The poor mans method is to clean it and then use RainX.  I've used both and actually prefer RainX (it is very easy to use, but you won't know the formulation but I would guess its similiar to OTS).  Again, it all depends what you are trying to do.  If you can elaborate more, I may be of more help.  Good luck.

Edit:  If its polyacrylamide you could functionalize the glass with -COOH and then use EDC/NHS chemistry to chemically bond the gel to the glass.

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Nolan's suggested method of plasma treatment and OTS is a good one. I can't think of a good reason to use NaOH to make your slips hydrophobic.

I've also used a reagent called "Coatasil", (available from Thermo Scientific), which works quite well at making glass hydrophobic.

NaOH is usually used before the addition of APES in order to make a hydrophilic surface. You can try RainX solution or DCMS solution (it is more toxic by the way) to make it become hydrophobic.