You can't convert ISA to PCI. And a PCI SCSI card would work just as well or better than an ISA card. Eliminating ISA slots eliminates some legacy support which can cause slight performance loss. That plus there are simply so few ISA devices created anymore, more people prefer to have extra PCI slots, and having ISA slots in addition to the PCI costs more to the manufacturer.
There are still many motherboards that do come with one, and sometimes two, ISA slots which are shared with the last one or two PCI slots (meaning you can use one or the other, but not both at the same time). The Abit KT7 is one.