First a virus requires a flaw to exploit. The republic would have to find a common flaw among all of the different droid versions then develop the virus that can be delivered to them en mass. The droids are AI so they could very well recognize the virus activity and eliminate it especially once the virus is recognized by the federation and distributes the signature. This means that all the effort and expense of developing the virus is countered quickly potentially before it does any damage.
Droids can always be memory wiped and reset. There are instances in the EU Where a slicer did rig droids to turn at specific times, or to take them over. One of the tools they use are viruses. But these are limited to a few droids usually. There is a specific objective that they are trying to achieve rather than forcing the TU to rebuild its entire army.
And finally Palpatine was pulling the strings with the TU. He did not want the war won early. And once it was time to take them on, the emperor preferred to stamp them out completely with a military victory. A hack would not have the same effect as having your forces completely annihilated by overwhelming force. A big part of winning a war is the psychological factor.
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