By using Latex Templates, is it possible that I am unknowingly disadvantaged.
Yes it's entirely possible that you are being disadvantaged here - it doesn't matter how pretty you make the CV if you can't get that "clean professional look" in front of a human!
The entire point of an automated parser is make it easier for the person reviewing the CVs to identify the ones that are worth progressing and what can be easily and quickly cut when there is large numbers of applicants. One that gets through mangled (assuming it gets through at all!) makes the job of evaluating that candidate infinitely harder and the harder it is to review the more likely it is going to get cut very early.
Sorry to say it but if a CV came through with the sorts of distortions you are talking about I probably wouldn't even bother to read it unless I'd got a very small number of candidates - and even then I'd be predisposed against it because I'd resent the extra effort involved in even reading it!
FWIW the only "look" aspect that I have ever considered when reviewing a technical CV is "can I easily find the info I need to see if the candidate warrants interviewing".
Pretty icons for skype account details/phone numbers/etc or fancy bullet points just aren't worth the effort IMO, I'd never discount someone for them but it wouldn't make me more interested in them in the slightest.
So do yourself a favor - apply the KISS principle and keep it clearly readable for both humans and our robot overlords, without the visual frills (and in whatever file format they want).
Especially if you think there is the slightest chance it's going to go through a parser! If you think you can add value with fanciness then the appropriate thing for that is to bring hard copies to an interview.
Are uploaded resumes/cover letters ever/always used?
If the company is asking you to upload a resume/cover letter it's because they have a use for it.
Given thousands of applications, is looking at uploaded resume not bothered?
As mentioned above when there are very large volumes of applications that's when parsers come in to play to allow the numbers to be cut down to manageable levels as quickly as possible - and that's why it's cruical to have your CV in a format that will stand the best chance of passing through them cleanly.