Yes, you're correct! When asking if a seat is available in places like cafes, common phrases include:
"Is this seat taken?"
"Are there any available seats?"
As for your question about "Is this seat empty?" it is grammatically correct, but it may sound a bit less common or natural in everyday conversation. People generally prefer using the first two phrases mentioned above.
Regarding your second question, saying "I found empty seats over there." is absolutely correct and natural. This phrase effectively communicates that you've discovered unoccupied seats and is commonly used in various contexts.