Of course to add to complexities for security a few things to consider:
a) Do any of your staff or your clients use public access networks, ie: wifi in a coffee shop, or the airport? If yes then non-SSL login to EE (or any web applications) is vulnerable to interception.
b) Do your staff and your clients, mostly in the case of Windows users, run full up-to-date AV/Malware scanners? Even if all of your access to a site is over sFTP/SSH, or httpS/SSL protected web pages, a keylogger installed on one of their systems via malware will pick up the URL and keys typed before the encryption happens between the client OS and the server.
c) on the same note as b) are any of your staff or your clients computers used by people other than your staff or clients? Have a friend that constantly was trying to figure out why malware and viruses were being found on his Windows XP test system in his office, turned out his wife was using that system for playing online flash games and a number of those sites constantly were installing over and over the same infections on the system. So do their wife/husband, kids/teenagers, or whatever use that computer at times?
d) Does the server/hosting provider/etc. keep detailed logs on all logins at the sFTP level for association of login vs. what was uploaded/deleted/downloaded from the site? If the server is self run by you or your clients (self-managed VPS/dedicated servers at a hosting provider, or even fully in-house), if so, are logs accessible to the people who have login access? or are logs collected on central/secure syslog servers keeping log data secure off the main server(s)?
e) Even if your hosting provider (like we do, and have without issue for over a decade) provide your initial login information via e-mail, how would you distribute that information to your staff and client? Do you do it by e-mail? unencrypted and/or free IM client traffic/services?
If that data was provided to you via a one-time secure web page access, how would you turn around and provide those details to everyone else? Would it again still be by the same email or non-secure IM conversation?
You would not want those details forever available on a web page as that leaves even our systems open to compromise allowing the normally one way hashed passwords to be visible in some context on a public web site, and even if it was you would need to distribute that URL or access method to the real sFTP/Site login data, in turn compromising the possible security of that data indirectly.
f) If the issue is a persistent issue, ie: you are not sure if its a hack via public access, or a malicious deed by someone on staff (ie: inside job), security products (if you are running on self managed systems) like http://www.tripwire.com/products/servers/ can take a base-line of all files on the system, details are stored in a secure database (or off server in a central server), and you can run periodic (daily) runs through specific data to see if changes took place. Which if you do research into security concerns for corporations, inside attacks are much more common and costly then external forms of hacking attempts at systems. Keep in mind on active web site projects this can be daunting, and separate products would need to be used to track database changes vs. file system level changes. These take a lot of management/monitoring on busy setups as you will find things like directories for caching/captchas/locations that allow image/file uploads will modify the base-line and will require likely daily review and tracking. All in all this works great for things like overall server/OS configuration files, not so well on groups of files that again change rapidly and normally through daily usage.
g) In the event an issue does happen, do you have contact with either the hosting provider, or in-house people that have the expertise to handle security concerns, exploit investigation, etc. to assist in the detailed diagnostics that maybe needed?
and last on my list for now, are scripts and files used in the site monitored with the given authors web site and updated timely any time major bugs or security fixes are released, and in general any time updates themselves are released. Usually the farther behind you are in keeping all web applications updated, the harder it becomes to both know about issues, get support, and upgrade quickly if there is an issue.
You can get incredibly detailed on the security side of things to the point it can actually get counter productive to a degree that it becomes less secure, or almost completely non-functional.
Sorry for the quickly done, but long ramble, probably will need to go back and clean this up a little once I am done with my current project tonight.