To block undeleters it's sufficient to fill space with "generic" data then delete the file
As for removing the chip and using an external programmers, some indeed expose raw memory over the pins (MTD chips) and there's no reasonable way to wipe the hidden areas (well, assuming you want a device that still works - otherwise there's the Cobra 6 method
), others have on-chip mappers (all SD cards including eMMC) which can have a TRIM command -- which however has historically been a major cause of bricks on some controller firmwares...
Motorola International 8700 (first phone sold in Italy to send SMS) [half bricked] > Acer ? [returned] > Siemens S35i [good] > Samsung SGH-? [stolen] > Nokia 3220 [mostly still OK] > Motorola RAZR [still OK] > iPhone 3G S [2 batteries worn out] > iPhone 4S [I gave up after iOS 7, still has 10 months of warranty] > Samsung Ace 2 i8160 [won at Samsung giveaway, still works fine, CM10.1] > Sony Xperia U [modified Sony 2.3.7]