not the icons 
see the games (sonic image) icon, this one is more easy to perceive... in the actual icon size, it is hardly possible to know "what is this icon about?" (hard to see a sonic here), more exactly:
same for the graphics one
while in a previous screenshot by you, they are more easy to recognize:
they are now (a bit) increased 
ah! found!
GUI Settings -> menus -> icon size
we are a bunch of geeks that don't know how to use gui's... sorry @Rebel450 
The "~/.e16/menus/menus_apps/Utility.menu" starts up guake in a separate terminal with:
exec "/etc/alternatives/x-terminal-emulator -e guake
Which should simply be:
exec "/usr/bin/guake"
Otherwise guake will terminate too if you close the terminal.
The big trouble is that there is no proper e16 theming documentation any more, if there ever was.
It's like re-inventing the wheel sometimes .... with all the searches and comparisons looking for a specific setting. 
Cutting my teeth on the padding of the menu-title in the light theme ...... gaaah !
that's not a (shipped) included app in elive, cannot fix , there's too many packages on debian that should be fixed otherwise lol
make a look to the file /usr/share/applications/guake.desktop (or similar), you would see the issue on the Exec= entry here, this is bad made, it should include an entry like:
Terminal=true
in case that requires a terminal, but running it that way is not correct and very hacky
so you should instead report the bug to the author of the package (if ships with a .desktop file) or to the debian maintainer of that package
there's a big documentation called .c files (ok joking 
, but is useful most of the times)
check my just other-commented thread, maybe there's the answer (and remember to purge caches if no effect)
The menu generator is now 4x times faster 
patch sent to upstream: e16/e16.git - Enlightenment DR16
Necroposting a tad here but, I just did find where this is set while I was trying to figure out how the pagers was being placed.
That's in the file '~/.e16/config--0.0.cfg' in the line:
"menus.icon_size=20" where if the value is changed and saved it will show.
NB.
Looks like I can influence the pager's position either directly using 'eesh win_op <windowid> <mr/sr> <x> <y>' or "move" as well as editing the XY values in the file "e_config--0.0.snapshots"