1) If it's a small site that you aren't sure if you can trust, then yes, I think it's safer to pay through Paypal. That way the site never sees your card info. That info is only exposed to Paypal, who you can reasonably assume do a good job of securing it.
2) Although I wouldn't be very worried about Paypal compromising your stored info, in principle I think it's probably safest if the info isn't saved into an account. When I make purchases through Paypal, I pay as a guest and enter the card info at the time of the purchase. My reason for doing that isn't so much for security, but still, just as a security concern it still might be the safest way to do it.
Big caveat though - you do have to be careful each time you type your card info that it's truly Paypal, and not a spoofed imitation. In that regard, it could be argued that having the info saved in a Paypal account could be better.
I do have a Paypal account but I only use it to receive money, I don't log in to it to make purchases. I've linked one card to my account because it was mandatory, but that only serves as a required "backup" funding source and never really gets used.
3) I don't know much about the portals.
