having two hard drives is essentially, no more or less secure than having one.
However if you are running windows with your Qubes partition encrypted and 'safe',
then Windows (and all of its rather large attack surface) would be like leaving
the screen porch unlocked so now the thief can come inside to look for a way in,
rather than standing in the road to look for ways in.
Rather, they could gain continued access to windows, and slowly chip away at
your Qubes OS while you are working in your Windows OS.
The only way to combat this (and do not consider me knowledgeable) would be to
switch HDDs every time you switch OS. These other users in this post definitely
know more than I do, but Im just trying to help where I can.
*This advice is only considering that you are trying to protect your data and takes no consideration for your privacy.
You are aware that you can install windows in qubes?
On the model of pc, I have the i7 with 16gb ram and an Intel SSD 545s Series
and it takes what seems like 15 minutes to boot the system. Ive attributed this
to the SSD. Go ahead and set +$100 aside for a NVMe m.2 SSD. What I currently have
is manageable, but sometimes becomes rather annoying. Mainly during startup and shutdown.