I had exeprienced the same issues in getting AdMob working together with storage using Phonegap/Cordova and a sqlite file with my db being copied from the apk into the db location.
I have tried the delay solution mentioned here. My observation was that to access the database with the correct data the window.openDatabase("xxx", "1.0", "xxx", 1000000); needs to be done before the AdRequest is created. This wasn't a solution in my case, since opening the connection again on another page where it is neded will result in the database being empty.
The way I solved this issue was with a plugin available at https://github.com/lite4cordova/Cordova-SQLitePlugin. It works exactly the same as the websql with the exception of opening the database in a different way (not much to rewrite if you have your queries already written). If you open it using:
var db = window.sqlitePlugin.openDatabase({name: "DB"});
it will use a DB.db file rather than the default 0000000000000001.db. This should prevent conflicts with AdMob. 2 things to watch out for:
The plugin needs ondeviceready to be trigerred not just document to
be loaded to open the db.
If you are coping an sqlite file you ship
with the apk, make sure to adjust the location where you copy it to.