The biggest injustice is that innocent private parties are forced to carry the costs of something that (allegedly) will benefit the public.
Investigations of crimes benefit the public, and so the public (taxpayer) should pay the costs of the investigation, not whatever private party the costs happen to fall upon. Taking this logic to its conclusion, in a fair and just society, if a law enforcement agency executes a search warrant, it should have to pay those affected by the search warrant the reasonable costs of that seizure (e.g. the cost of renting and deploying an acceptable alternative until the equipment is returned, or the cost of lost business if it is a purely for-profit organisation and loss acceptance appears to be the cheaper based on the information available to the business at the time). This wouldn't apply if the court was satisfied following a contested hearing that the person having assets seized was a party to a crime being investigated.
While the above would be fair, it is not how the law works in many jurisdictions, because politics works on what politicians can fit in a sound bite (lower taxes! more law enforcement on the same budget!), not necessarily what is fair to minorities like innocent parties having their equipment seized.