I see what you meant now. Yes, you had the right idea. Modifiers can't trigger hotkeys in this version of HotkeyNet. I made this limitation to try to prevent frustrating user errors, because if you make a hotkey that gets triggered by pressing LCtrl, then by default, you disable LCtrl on your keyboard, and I thought this would cause a lot of headaches for people.

Therefore, if you want LCtrl Numpad1 to trigger a hotkey, you have to tell HotkeyNet that the key combination LCtrl Numpad1 is a trigger. For convenience you can write a lot of trigger combinations at once. For example, suppose you want to define these three hotkeys.

LCtrl Numpad1
LCtrl Numpad2
LCtrl Numpad3

You can write that like this

<Hotkey LCtrl Numpad1 - Numpad3>

And suppose you want to define these additional three hotkeys

LAlt Numpad1
LAlt Numpad2
LAlt Numpad3

You can add them to the previous definition like this:

<Hotkey LCtrl Numpad1 - Numpad3; LAlt Numpad1 - Numpad3>

Here's how to apply this info. In this case, you want hotkeys for all the number pad keys with both LCtrl and LAlt. I'll write it as two separate definitions to make it easier to read, but it could also be combined in one definition. I'll remove LCtrl and LAlt from your original definition and add a new definition.

Code:
<Hotkey ScrollLockOn A-Z, NumPad0-NumPad9, Space, 0-9, Divide, Multiply, NumpadMinus, NumpadPlus, except w,a,s,d,q,e>
<SendLabel w1, w2>
<Key %Trigger%> 

<Hotkey ScrollLockOn LCtrl Numpad0 - Numpad9; ScrollLockOn LAlt Numpad0 - Numpad9>
<SendLabel w1, w2>
<Key %Trigger%>