When you upgrade a ship (via the map, not the designer), there's a checkbox on that screen to do all of that class at once.

In other words you cannot mass upgrade a 'fleet', but you can mass upgrade a particular kind of ship.

Personally, i never use that option because the upgrade option also doubles as a 'repair' button!!

Also there is no point in upgrading ALL the ships of that design when only a few of them might be facing iminent combat, then by the time the rest are facing combat, you might have developed a new useful upgrade tech!