Are you sure it's returning all the rows, and not just all the ones that match the Div_Desc value?
It looks like the problem is this part:
([WWALPH] like '" + querySeed + "%')
When querySeed is blank, this will evaluate to:
([WWALPH] like '%')
which will match every row in the table. You might want to try something like this:
string wwAlphMatch = string.IsNullOrEmpty(querySeed) ? " = ''" : "like '" + querySeed + "%'";
string customQuery = " where ([WWALPH] " + wwAlphMatch + ") and (BuyerNumber in (Select BuyerNumber from Lots where [Div_Desc] = '" + querySeedDiv + "'))";