I have a custom pickaxe that mines the ore and all ores around it and I'm not sure how to account for Silk Touch.

Here is the code:

public boolean onBlockDestroyed(ItemStack par1ItemStack, World par2World, int par3, int x, int y, int z, EntityLivingBase par7EntityLivingBase)
    {
	super.onBlockDestroyed(par1ItemStack, par2World, par3, x, y, z, par7EntityLivingBase);
	if(!par7EntityLivingBase.isSneaking())
	{
		String st1 = Integer.toString(par2World.getBlockId(x, y, z));
		String st2 = st1 + ":" + Integer.toString(par2World.getBlockMetadata(x, y, z));
		if(Arrays.asList(this.ores).contains(st1) || Arrays.asList(this.ores).contains(st2))
		{
			//par2World.destroyBlock(x, y, z, true);
			this.repeatMine(par2World, x, y, z);
		}
	}
        return true;
    }

public void repeatMine(World world, int x, int y, int z)
{
	for(int i = -1; i <= 1; i++)
	{
		for(int j = -1; j <= 1; j++)
		{
			for(int k = -1; k <= 1; k++)
			{
				String st1 = Integer.toString(world.getBlockId(x + i, y + j, z + k));
				String st2 = st1 + ":" + Integer.toString(world.getBlockMetadata(x + i, y + j, z + k));
				if(Arrays.asList(this.ores).contains(st1) || Arrays.asList(this.ores).contains(st2))
				{
					world.destroyBlock(x + i, y + j, z + k, true);
					this.repeatMine(world, x + i, y + j, z + k);
				}
			}
		}
	}
}

Use

EnchantmentHelper#getEnchantmentLevel(enchId, itemStack)

where

enchId

is the ID of the enchantment (e.g. Enchantment#fortune#effectId) and

itemStack

is the ItemStack you want to check (in your case the stack passed as parameter in your method).

The method returns 0 if it isn't enchanted, else it returns the level of the enchantment.