STEP 1: FTP/SSH to your device.
STEP 2: Find this file /Applications/Cydia.app/package.js
STEP 3: Search for this, you may find it in line 209:
if (depiction == null)Change it to:
if (depiction == null || true)STEP 4: Now enjoy an ad free Cydia.
Here is the screen-shots before and after:
Of course if you want to see the ads again you simply have to reverse step 3.