Emailing illustrator file from one computer to another

Is this saved as an .ai file? (i.e. not PDF)

What you're describing can happen if you open the PDF side of an .AI file. this shouldn't happen normally, but there may be a bad file association on your receiving computer that's mistaking the file as PDF. Try open the file from within Illustrator, selecting "Enable > Illustrator (.ai, .ait)" instead of "All Readable formats". If it opens differently, there's a problem with your system's file associations.

I have never encountered an email server literally altering an Adobe Illustrator AI file to where everything is flattened. Wouldn't that require the server to somehow open and edit the file to flatten any live effects? Or is the AI file being converted to a "flat" pixel based image? I guess I'm a little confused by the issue.

Aside from that, many Illustrator AI files can get pretty large in size. Many email servers will have file size limits on attachments. If I have to email an AI or AI-enabled PDF to someone I'll usually upload the file my Dropbox account and send the person a link to that file so they can download it directly.

Just a reminder, one alternative to emailing is saving it as a cloud document (not sure if that works for your workflow, but it may be easier)

Zip it before attaching or use filesharing and send a link is probably better.