A little background:
As of PyDev 2.3.0,
pep8 is integrated in PyDev by default, even shipping with a default version of it.
Open Window > Preferences
It must be enabled in PyDev > Editor > Code Analysis > pep8.py
Errors/Warnings should be shown as markers (as other things in the regular code analysis).
In the event a file is not analyzed, see https://stackoverflow.com/a/31001619/832230.