There are some manufacturers that pay more attention to it, I'd say R&S is top in this category from what I've heard, but it's also not a difficult modification to make. The fan is generally just attached to the case and fixed to the board with a standard connector, so while you have to crack open the scope, you don't really have to remove anything but the fan in most cases.
Since they use standard computer case fan sizes, you can find a lower sound level one with similar performance specs (flow volume is usually given, static pressure matters and people will insist it's extremely important but in my experience as long as the flow path isn't too obstructed, it's not a big issue to use an rated for less pressure), then swap it in.
I would verify what kind of fan is in there to match/exceed specs, then verify that the pinout of the connector is the same - I've run into a few test equipment fans that have two pins of three swapped from the normal PC configuration.
Also worth mentioning that physical obstruction of the airpath, especially with hard edges (heatsinks, fan grilles, etc.) will increase noise and are generally harder to work around. Sometimes a small spacer to keep the grille at a distance is helpful for this, but it rarely makes a big difference, and you do have to make sure you still have clearance on the opposite side.