I deposited some ETH/BTC and I can see it under my Balances. Does the ETH/BTC not count towards my USD balance?

It might not be obvious at first sight, especially if you have experience with trading on the spot only. The short answer is NO, your ETH/BTC doesn't count to your USD balance. You need to swap it here to get USD and then you can trade all futures:
https://scalpex.com/trade/ETHUSD-SPOT
https://scalpex.com/trade/BTCU...

Scalpex is a crypto derivatives exchange. So you buy and sell perpetual futures contracts for underlying crypto against USD, not crypto itself.

Your USDT (though this is an ERC20 token), being a stable token tied to USD, counts directly to your balance available for trading.