1-) I've .NET GUI app. Yes, you have AutomaticUpdater control and wyUpdate.exe but i dont want to use them. Is there any way that i can check updates?
No. You need to use at least wyUpdate. That's what does the update checking and the update installation. The AutomaticUpdater is optional. See: http://wyday.com/wybuild/help/walkthrough.php
2-) As I recall, wyUpdate is open source. What if someone figues out the contents of client.wyc? Client.wyc includes the update folder link. What if someone finds that URL and downloads all the update data?
To limit updates to paying customers see the articles we've written: http://wyday.com/wybuild/help/limit-updates.php