I never reply to editor's and conference organizers' mails, since I somehow always thought that they are automatically generated and replying just to thank would be considered as spamming, since they probably write to hundreds of people.
But is this really true? Do editors prefer not to get trivial replies to their email? Are their emails really automatically generated, or just some parts of them?
In the case of editor's mails, some will need some form of response, some will not. If you receive mails from an editor requesting information concerning a manuscript you have submitted, you will obviously have to reply.
Since most journals use electronic manuscript handling systems, many mails will be generated automatically as reminders or to tell you something about the status of your manuscript. Unless there is a specific question for you to respond to, you do not have to respond. Editors handle lots of manuscripts and and the automated systems generate lots of mail for each as information to authors, reviewers and the editor. Responding to mails that do not request information is not wrong but completely unnecessary and the editor will likely glance at it and go on. Obviously the situation would get out of hand if everyone responded to all mails in such a system so just focus on those that request a response, that is all that is expected.
As for conferences, I would expect a similar scenario. Many mails will be information and only those that request information need to be answered.
The bottom line is, you need to make sure you answer the mails where you are requested to do so but the rest can safely be left as the information they were intended to convey.
