When SiN Episodes: Emergence was first released, 4:3 resolutions were commonplace and SteamPipe wasn't a thing yet. The menu was designed for 4:3 resolutions, and still is. Because of this, the menu tends to break on widescreen resolutions.
Prior to SteamPipe, files in the SE1 folder overwrote the contents of the GCFs, and modifying the game was as simple as modifying any other Source engine game. Now, however, the contents of the VPK files always overwrite the contents of the SE1 folder, and the game also lacks any kind of custom folder.
The game has an alternate depot called 'loose' in which all files are loose and the VPK format isn't used.

Outdated Info:
Because of this, in order to use mods in the game, you now have to modify the _dir.vpk files in order to change the names of the files inside. When the game can't find the files in the VPK, it will look in the SE1 folder and load the modified files.

Right-click on SiN Episodes Emergence in Steam and select properties. Select the beta tab and, in the dropbox, select the beta labeled 'loose - '. This will download a version of the game which uses only loose files and doesn't rely on vpk files.

After the download completes, reopen the properties dialog if you've closed it, and select the tab "Local Files". From here, press "Browse local files..." to open your Sin Episodes folder.

Once that is done, download this file and extract it to the SE1\ folder within the SiN Episodes Emergence\ folder, replacing the existing file.
Dropbox[www.dropbox.com]
Gamebanana[gamebanana.com]

Finally, you'll end up with a menu which looks proper on 16:9 resolutions. It will, however, not work if changing back to a 4:3 resolution, and will probably only just be passable on 16:10 resolutions.

These instructions are old and shouldn't need to be used. The method is very similar to old methods for adding custom content to the original Left 4 Dead.
Please don't do this.

First, locate your SiN Episodes Emergence folder. Unless you've set up a secondary or tertiary install location for games, this is most likely something similar to:
C:\Program Files\Steam\Steamapps\common\SiN Episodes Emergence\

Once located, open the folder, and the folder titled "vpks" within. Inside that folder, find depot_1304_dir.vpk. Copy this file to somewhere safe, and then open the original in a text editor. A powerful text editor such as Notepad++[notepad-plus-plus.org] is recommended for this, but any will do. If using Microsoft Notepad, however, keep in mind that it will take a long time to load the file.

Once open, search the file for "clientscheme" without the quotes, and replace one letter with something else. For instance, you could turn it into "2lientscheme". IT IS VITAL THAT YOU DON'T CHANGE THE SIZE OF THE FILE. IF THE FILE ENDS UP WITH ANY MORE OR LESS CHARACTERS THAN IT HAD ORIGNALLY, IT WILL NOT WORK.

Once that is done, download this file and extract it to the SE1\ folder within the SiN Episodes Emergence\ folder.
https://www.dropbox.com/s/tw45q6hcsqlokih/menufix.zip?dl=0

Finally, you'll end up with a menu which looks proper on 16:9 resolutions. It will, however, not work if changing back to a 4:3 resolution, and will probably only just be passable on 16:10 resolutions.