ls is a technical unix command, not a user tool (which "clicki-clicki" mouse user knows ls?). ls must show everything, and it follows the kiss principle (keep it small and simple).
Using a graphical dir browser like Dolphin could hide such unreadable contents, that would be nice, as normally users don't need to see that. Should be a config option.
Browsing a server over the network is about 20 years younger "command", solving completely different needs, and it would help security a bit if shares not accessible are not seen by a user. But by the time Microsoft reinvented networking, they did not have the slightest clue about security (and I'd say that only started with Win7, where a user can work as user not admin). Maybe we'll see that improvement once someone at Microsoft gets the idea. Or maybe the Samba team can implement a setting to hide this, and later MS adopts it as it's clever.