In ion implantation dopant ions are directly bombarded into the semiconductor (silicon for example)? But if say P ions (P+) were implanted then it does not have an extra electron to donate into the silicon. How does the process work then?
Yes, the ions carry charge. However, the substrate is grounded so that current flows to keep the substrate neutral (and to measure the implanted dose). Otherwise a potential would rapidly build up (possibly up to the accelerating potential), changing the implant profile and/or causing arcing. (As an aside, this causes some difficulties when implanting or performing ion beam analysis on insulating substrates - usually a thin conductive carbon or metal coating is needed to prevent arcing.)
Once the impurities are implanted, the substrates have to be annealed to eliminate all the damage to the lattice from the implant, allow the dopants to move on to lattice sites, and thus become active.
Ultimately, whether the ions are singly charged (positive or negative), or multiply positively charged, makes no difference in the end result.