Everyone knows the publishing industry is a bit chaotic just now. Barnes & Noble is up for sale and e-books are growing at a rapid clip. (But don't ask ME just how fast, or which is in the stronger position out of Apple and Amazon, or even how viable the market is for non-erotic romance e-books like, oh, mine--do I look like I have a crystal ball?)
Fantasy author Jim Hines has a post up addressing some of these changes from a writer's point of view by describing how much has changed about the submissions process since he started writing in 1995. I've only been writing seriously since 2001 and didn't start seeking publication till 2003, so I can report that querying is different than it was even five years ago. Then I sent a lot of paper queries and even manuscripts. Now the vast, VAST majority of editors and agents prefer electronic submissions. A few still ask for paper. Should you bother with them? Speaking for myself, I'll send a paper query to an agent if said agent has a solid web presence and seems tech-savvy, because they're probably avoiding email queries to cut down on the flood of submissions. But if I think there's even the slightest possibility they just don't want to accept change, forgeddaboudit.
I was delighted to switch from Courier to TNR and to replace underlining with italics, but there's no way I'm ever going to break my high school typing class habit of putting two spaces after a period that I learned back in 1989. So I do a find-and-replace just before submitting.
In general, things are changing fast, and while I expect the industry to eventually settle into a New Normal of some kind, it'll take awhile. Don't assume the way you've always done things is still industry standard, especially on things like paper vs. electronic, how to measure word count, preferred fonts, etc. Check your targeted agent or publisher's guidelines and adjust accordingly.