I just found out my honda st1300 was an old police bike bought at an auction. Is this bad?

I searched the VIN and found it on this website:
https://www.govdeals.com/index.cfm?fa=Main.Item&itemid=10749&acctid=685

It was clearly not in great shape but it's been restored (not mint by any means, but in good shape) and runs well now. I ran a KBB vin check and it doesn't have any record of being a government vehicle which I found odd. It has 32k miles and was clearly sitting for awhile in South Carolina where it came from, as you can see from the pictures on the website.

In terms of value, is my bike worth less because of being government owned, more, or the same?

If the bike runs well, the problem is that you are making yourself unhappy. Usually police bikes get professional maintenance and regular oil changes. Also, police bikes are made to idle and run radios, lights and electric winter gear, so they have heavy-duty cooling systems, beefy alternators, and heavy-duty batteries. Maybe it's better than a civilian bike.

While it was government owned it was used "hard" but it also received top maintenance (likely).
Its value is much less than a "Normal" civilian bike, merely because of the heavy use.
You need it surveyed by a Licensed Tech (Dealer) for hidden problems.

Nobody really cares, Sparky. It's just that a motorcycle used in police service will usually have more miles on it than a similar privately owned bike would have. Police bikes are typically well maintained and not abused.

Honda ST1300
http://powersports.honda.com/...t1300.aspx

PA Police Motorcycle
http://powersports.honda.com/...00/pa.aspx

your reference to 2006 model
https://www.govdeals.com/index.cfm?fa=Main.Item&itemid=10749&acctid=685

If the one you link to is yours, it is in need of repair, If already repaired, then if mileage and oil and noise is good and passed certification for safety, then it is ok for travel, would not use for racing, only for touring.
.

32000 is low miles for one of those engines particularly as it should have been well looked after. It is unlikely to have suffered any more abuse, if any at all, compared to a privately owned bike. If it is running well then no need to be concerned about it or its value

EDIT - having looked at the pics I can confidently say that it is not Police Specification and in that condition is worth almost nothing