True, but unless they think someone at the colo is going to tip off the owners, taking 10 minutes to figure out which machine hosts which site shouldn't be an issue. With a warrant, I imagine the colo would be willing to look up the mapping from company -> rack/server being leased.
Keep in mind that the FBI agent-in-charge's perceived cost for pissing off some small web companies is pretty low; their perceived cost for tipping off whoever they're after, and blowing the entire operation, is much, much higher.
I wasn't addressing the egregious police-stateness at all, one way or the other (which I suppose is downplaying it, by not addressing it, but that wasn't my intention). I think that there should be incredibly strict bounds on what can be seized without a warrant, and still rather strict bounds on what can be seized with a warrant, but I don't know whether this case overstepped those bounds.
For example, I believe it's illegal to take information which was coincidentally seized along with legitimate evidence subject to a warrant, and use it in an unrelated case. I'm strongly in favor of such laws, to discourage "fishing expeditions", where law enforcement uses a legitimate warrant to seize a bunch of unrelated material that they're interested in using for other purposes.
However, I suspect if you walk into a data center where some malicious customer is doing something illegal, probably that customer has tried to make it harder to connect them to what they're doing.
Also, I don't know about this case, but there are lots of small hosting companies that lease servers from other companies, and the staff at the colo only know the lessor, not the lessee. They wouldn't have any access to the hosting company's customer database which might map customers to servers.
Besides, the FBI has to worry about low-probability cases like, what if one of the employees is a friend of, or paid off by, the bad guys? Or what if the bad guys are somehow monitoring the facility?
The FBI has a legitimate goal of seizing the evidence they need as quickly and with as little notice to the bad guys as legally possible.
Did the FBI act wrongly in this case? I don't know enough to tell.