Yes, the atoms that loose electrons are ionized. That's what ionization means. The atom now has more positive charges in its nucleus than electrons bound to to it locally. We call this net positive charge a hole and treat it like a particle because it can move around. The electron that enters the conduction band is delocalized and forms a state bound to the entire crystal, but the atom it leaves behind stays localized.
Because the conduction electrons are essentially free, they move and bunch up in places different then where the holes are. While the entire solid may stay globally net neutral, it is not locally neutral. The non-zero space charge leads to an electrostatic potential known the built-in voltage which effects charge transport. These effects are very important in semiconductor heterojunctions such as in diode lasers, transistors, quantum well devices, etc.
The picture gets more interesting if you dope a portion of the semiconductor with donor or acceptor atoms. With a donor atom, when the electron is freed to the conduction band, a hole is not left behind because the donor atom already had one extra electron compared to its neighbors. But the atom left behind is still net positively charged. So you get a fixed positive ion (not a mobile positive charge, i.e. a hole), which also contributes to the space charge. In the most general form, the space charge is the sum of the conduction electron distribution, the hole distribution, the positive ion distribution (ionized donor atoms), and the negative ion distribution (ionized acceptor atom). Not every atom gets ionized. It depends on the temperature.