The following methods already handle these cases

CraftBukkit-Patches/0015-Orebfuscator.patch

@@ -1,4 +1,4 @@
-From 2617973d6c96afdf7aed70fbb3fc328f031431ae Mon Sep 17 00:00:00 2001
+From 7cbaaecf6d7a0ff82d824f3416d45ac80c68aaaf Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Thu, 16 May 2013 18:51:05 +1000
 Subject: [PATCH] Orebfuscator
@@ -173,7 +173,7 @@ index 67477f4..e5004b3 100644
          }
 diff --git a/src/main/java/org/spigotmc/OrebfuscatorManager.java b/src/main/java/org/spigotmc/OrebfuscatorManager.java
 new file mode 100644
-index 0000000..b4d66f6
+index 0000000..e4d621a
 --- /dev/null
 +++ b/src/main/java/org/spigotmc/OrebfuscatorManager.java
 @@ -0,0 +1,211 @@
@@ -360,7 +360,7 @@ index 0000000..b4d66f6
 +
 +    private static boolean isLoaded(World world, int x, int y, int z, int radius)
 +    {
-+        if ( radius > 0 && y > 0 && y <= world.getHeight() && world.isLoaded( x, y, z ) )
++        if ( radius > 0 && world.isLoaded( x, y, z ) )
 +        {
 +            return isLoaded( world, x + 1, y, z, radius - 1 )
 +                    || isLoaded( world, x - 1, y, z, radius - 1 )
@@ -375,7 +375,7 @@ index 0000000..b4d66f6
 +
 +    private static boolean hasTransparentBlockAdjacent(World world, int x, int y, int z, int radius)
 +    {
-+        if ( radius > 0 && y > 0 && y <= world.getHeight() && !Block.l( world.getTypeId( x, y, z ) ) /* isSolidBlock */ )
++        if ( radius > 0 && !Block.l( world.getTypeId( x, y, z ) ) /* isSolidBlock */ )
 +        {
 +            return hasTransparentBlockAdjacent( world, x + 1, y, z, radius - 1 )
 +                    || hasTransparentBlockAdjacent( world, x - 1, y, z, radius - 1 )