Yes, you can turn EVERY upgrade on/off,except, I'm afraid, the second Suit style. Meaning, you'd always be stuck with the Varia Suit 2, only the palette would change if you deselect the other suits. Also, you can't really turn on/off the Unknown Items until you get the Fully Powered Suit.
As for the Weapon Effects: You CAN turn everything / anything on/off. Want to see the green Plasma Beam before it's "iced" blue? You CAN do it! The purple Wave Beam? Yes! You have to get the patch.
*looks at rules page*
But since it seems that we can post links to ROM sites... and so far I've only been able to find the patch from a ROM site...
*looks around warily*
I'll wait for confirmation before posting the link.
As for the Weapon Effects: You CAN turn everything / anything on/off. Want to see the green Plasma Beam before it's "iced" blue? You CAN do it! The purple Wave Beam? Yes! You have to get the patch.
*looks at rules page*
But since it seems that we can post links to ROM sites... and so far I've only been able to find the patch from a ROM site...
*looks around warily*
I'll wait for confirmation before posting the link.