Your problem is probably the same as this known issue :
Issue 416148: Omnibox Displays Javascript Bookmarklet Suggestions.
Steps to reproduce the problem:
1. Create a bookmarklet
2. Type "javascript" into the omnibox
3. See that the omnibox is filled out with the entire bookmarklet script
What is the expected behavior?
Do not include bookmarklets (anything
that starts with the javascript: protocol) since a user would not
manually type that out as an option
What went wrong?
Typing "ja" shows expected results based on
previous searches and visited pages. Typing an additional "v" fills up
the entire omnibox with a bookmarklet script, making it difficult to
see what has already been typed.
This is marked as fixed and verified on November 3, 2014, on
Windows 7,40.0.2209.0 (Official Build) canary.
The fix itself is mentioned here as committed.
So it seems like you only need to wait for the next update of Chrome.
chrome://history/
, or (2) be able to turn on and off their display without removing them from history?