Very simple set-up:
Visual Studio --> Add New Item --> List Definition. Type: Document Library. Besides that - no changes. Deploy.
Result:

As you can see: No "configure incoming e-mail settings" link.
When I create a document library the regular way (e.g. Site Actions --> New Document Library) I get the wanted result:

How to I get the "Incoming e-mail settings" link on a document library deployed via Visual Studio?
EDIT (thanks to Falak):
The solution is to add (even if only a dummy) SPEmailEventreceiver to the list. So if you do this:
public class MyMailEventReceiver : SPEmailEventReceiver
{
public override void EmailReceived(SPList list, SPEmailMessage emailMessage, string receiverData)
{
base.EmailReceived(list, emailMessage, receiverData);
}
}
and the elements.xml:
<?xml version="1.0" encoding="utf-8"?>
<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
<Receivers ListTemplateId="xyz"> <!-- add the correct template id here -->
<Receiver>
<Name>MyMailEventReceiver</Name>
<Type>EmailReceived</Type>
<Assembly>$SharePoint.Project.AssemblyFullName$</Assembly>
<Class>myAssembly.MyMailEventReceiver</Class>
<SequenceNumber>10000</SequenceNumber>
</Receiver>
</Receivers>
</Elements>
Voilá, I have the incoming e-mail settings link in the document library settings.