The extra price for sitting versus standing is common throughout Italy and not just in Venice, and applies to locals and tourists alike. It covers the cost of waitstaff - who are usually paid more than they are in the U.S. - and changing/laundering of linens (tablecloths and napkins) which are more commonplace at even casual cafes than in the States. That's why you see most Italians having their morning joe standing at the bar.
Consider that it's a pittance compared to tipping percentages expected here as well?
Also, prices are ALWAYS going to be highest at prime spots such as St Mark's in Venice. We have a coffee break several times a day in Italy to rest our feet and use the 'facilities' but we choose cafes away from main attractions. Besides being less expensive, they're usually more pleasant, and waitstaff tend to be less hurried and more amiable.
And oh yes, soft drinks are usually more expensive than wine, coffee or sparkling water so when in Rome…
Anyway, we've come to love those daily breaks, and have no issue with paying a little bit more for the experience. It's certainly beats the long list of taxes and extra fees attached to many U.S. hotels these days.