Prepare a PDF/JPG layout for your proofs and include on this the version (eg. 01A), the date, the name of the client and your intellectual property info with your own contact details. If you're worried about clients using the logo drafts, rasterize them and add them to that digital PDF/JPG proofs (I send both.)
With that system, the client can easily refer to the proofs that were accepted or changes he wants to revert to.
This question has some answers in the url below.
I keep my files on my hard disks, and backup hard disks. I refer to the proofs system above if I need to compare versions. These proofs are always in their own folder named "0-proofs", and use my convention naming system.
How to name files: What is your file naming convention you use for version control?
Use a backup system for your archives; I use 2 external hard drives and one is a backup of the first hard drive. Change them every 2-4 years.
Your client's archives
For your clients, only send them the vector files once they are fully approved and paid. You can share a Dropbox with them and put your files there but honestly, I only do this with clients who have a lot of projects.
It's their responsibility to archive the files you send them and pay for the resources required for this. Suggest them to archive these files as they receive them. If they need them again someday, you can resend them to the clients for free or make them pay for the time it takes to find back the archived logos.
Emailing the proofs and final files
I use "hightail" to send my files; I can get a receipt when they were downloaded and leave them there for a specific period (2 weeks, 3 months, etc.) It's also useful because you can use their apps to upload the files and compress (or not) entire folders simply by right-clicking on the folder and uploading them; it acts a bit as sending emails, you can add a subject, and message with your files. The client doesn't need to have an account with Hightail to download them. Very clean way of sending files.
You could also have a look at Hightail Space; you can upload proofs there and use this space a bit like Basecamp. Your clients will be able to leave comments exactly where revisions need to be done, a bit like adding comments on a PDF. But they'll need to register to a free account though.
You could always look at online tools such as Basecamp. I personally hate it and find it messy. I find it easier and faster to use Hightail and emails for communication.
How to send the logos
A similar question was asked in the url below:
Industry standard file format deliverables for logos?
In general, send vectorized logo that have been cleaned-up and where the fonts are "outline." You don't send fonts or editable files besides the vector itself. Yes, another designer could open these files one day but that's normal.
Passwords on proofs or final files
No, don't add passwords! That will hard to manage for you and annoying for the client. When you'll provide final files, you have to expect they might be used by other designers or printers.
For your proofs, you protect them by adding your intellectual property tag and by sending files that will be hard to vectorize back (eg. rasterized, and not too big PDF/JPG.)
If you don't rasterize your vector logos and send a PDF, they're quite easy to extract.
PS: My system is the same as the ones that were used in agencies and print places where I worked. That's what they used to make their invoicing system, archive system (digital, films and plates), and all the communication easy to find and to refer to. When you'll end up with thousands of files, you will be happy to have adopted a very strict naming convention!