I own a Baja 25 Outlaw that has a low water pick up and boat in Florida where it is not unheard of to rub the "muddy" bottom with your outdrive! And with the low water pick up we all know what happens next! So my question is can the low water pick ups be plugged?

You would have to drill the side water ports in order to plug the bottom ones.

Ok drill new side ports or enlarge existing ones? And any suggestions for plugging the bottom ports?

I suggest you swap lowers. The low water pickup legs are in demand.

Just swap with someone with a standard pick up I would have killed to trade you a couple weeks ago, I had to drop $1300 on a used one because I had to have a LWP that day!! even though you can find them all day long for $800 on OSO & ebay.

I have a std. pick up lower but about an inch is broken off the bottom of the skeg Ill trade you + some cash of your interested just so I have a spare LWP.

Does it already have side water ports?? If so it would be a DWP and just have holes in the nose of, instead of slots below the bullet. If it is DWP just plug the holes with epoxy. If it is a true LWP you would need to drill the side water ports and plug the lower slots with an epoxy or all metal, something like that. Or install a nose cone that would cover the LWP, but you need to create ports in the sides so water can flow through the drive.
But it may be a better route to swap out the lower for a side water pickup.