Holes would be places where the ionization doesn't work. Holes would also mean you need the same vacuum conditions on both sides, which is often not wanted.
The foil does not need a positive charge. The approach works based on the huge size difference between electron orbitals and the nucleus. Many nuclei pass through without large scattering (->Rutherford experiment), most electrons do not.
Fully ionizing large atoms like lead for the LHC is done in multiple steps. The source provides Pb27+ (55 electrons left), this is accelerated to 4 MeV per nucleon and shot through a stripper foil. While many charge states are produced, the most likely one is Pb54+ (28 electrons left). This is accelerated to 6 GeV per nucleon and shot through another stripper foil, removing the remaining electrons.