Several reasons. First, there were already AGM-88 HARM which were dedicated anti-radiation weapons, and more capable in that role.
Second - the AIM-54 was not compatible with anything but F-14 fire control system. So the hypothetical anti-radiation AGM-54 would be only used by F-14, which were't exactly well-adapted for SEAD job. Some kind of adapters PROBABLY could be designed to allow F/A-18 to use it... but why bother, if AGM-88 was available?
Third - the AIM-54 was costly, complex to maintain, and "uncommon" missile. No one besides USN and Iran ever used it. So maintaining the AIM-54 would require having a lot of highly trained personnel specifically to service those missiles. Hardly a good idea, considering that such trained specialists are always in short supply.