“Thank you so much for all the business that you have given us throughout the years.”
Business should be singular. See note 1.
“Thank you so much for the business that you have provided throughout the years.”
This is OK. A more natural way to say this is:
Thank you so much for the business you have given us throughout the years.
“Thank you so much for supporting us through your patronage.”
OK as-is.
“Thank you so much for supporting us through your business and by helping us in the kitchen.”
This should be in the kitchen.
There are exceptions, but normally when it is inside an enclosed area you would use the preposition in.
“Thank you so much for your patronage at our restaurant. ( what is the preposition for patronage? At, for or towards?).”
At is correct.
Note 1
Business can mean the business itself as an entity, or it can mean patronizing the business by buying their product or service. The business itself is a count noun. Patronizing the business is not a count noun, so you can not use the plural.
I do business with five businesses.
The first ‘business’ is not a count noun. The second ‘business’ is a count noun.
I would probably say
“Thank you so much for your patronage of our restaurant.“
This sounds like a message to your restaurant’s customers so that context is already established. I would probably phrase this simply and directly as
“Thank you so much for your support over the years.”