I found the solution! I found out that, collation has impact only for ordering. I'm using fulltext search so I need to change fulltext indexes. Here is how I did if anyone else need do the same..
IF EXISTS (SELECT 1 FROM sys.fulltext_indexes WHERE object_id = object_id('Product'))
DROP FULLTEXT INDEX ON [Product]
DECLARE @create_index_text nvarchar(4000)
SET @create_index_text = '
IF NOT EXISTS (SELECT 1 FROM sys.fulltext_indexes WHERE object_id = object_id(''[Product]''))
ALTER FULLTEXT INDEX ON [Product]([Name] Language 1051, [ShortDescription] Language 1051, [FullDescription] Language 1051, [Sku] Language 1051)
KEY INDEX [' + dbo.[nop_getprimarykey_indexname] ('Product') + '] ON [nopCommerceFullTextCatalog] WITH CHANGE_TRACKING AUTO'
EXEC(@create_index_text)
ALTER FULLTEXT CATALOG nopCommerceFullTextCatalog REBUILD WITH ACCENT_SENSITIVITY=OFF;
The language code 1051 is for slovak language, you can find your code here: http://technet.microsoft.com/en-us/library/ms176076.aspx
Hope it helps!