It depends on what do you mean by "effectiveness".

Prizes pay out rewards whose value in resources matches the resources value of the troops that you've lost. So, in a simplified example, if you lose 1000 Marauders (which is 90k/150k/60k of gold/lumber/rum), you might get back 24 Frigs (the same amount of gold) with some leftover lumber and rum. Keep in mind that this is just an illustration; the actual system is more complicated, and also Plarium's secret, and we don't know it in depth.

So, if you're asking about "effectiveness" in terms of getting rewards, then there is likely no difference (the res value of common Marauders and pardoned ones is the same). Further, there was some speculation that the Brethren and/or pardoneded troops count as less than common and veteran ones in terms of Prizes' rewards "bank", but I never saw a confirmation of that.

If, however, you mean "effectiveness" as "the fighting ability", then they are slightly more effective. Pardoned units are 5% stronger than their common counterparts, so you'll need fewer of them to bring down the same Prizes and get the same experience.

Note that "needing fewer troops to bring down a Prize", combined with "rewards match what you lost in res value", means that you'll accumulate fewer resources from each Prize, so you'll need to attack more Prizes for the same rewards.

Personally, I think it's wastefull to pardon Pirates and Mercenaries. The best value for pardoning, in my opinion, is the lower rum consumption of troops, which makes it most valuable for the strongest offensive troops, because lower rum consumbtion means that you can send more of them against Bastions and Presidios (both of which have rum consumption limit for the units being sent to attack them). This, however, affects only the strongest players and BHs, and it might not be interesting to anyone else. But, still, the effect for Prizes is minimal, making it a bit wasteful (IMO, of course).

Crowbar I completely agree on the not pardoning pirates to do prizes but as far as doing the Adventures then pardoning Marauders to do Offensive Adventures then yes it is well worth pardoning them and using less to gain more in troop value. And using pardoned Chineese troops to do the Deffensive Adventures also produces the same results.

I like your way of thinking and, yes, it does pay off to some extent. You get 5% stronger Marauders, so you'll need 5% fewer of them (not exactly, but close).

My only issue with it is that 1 Jaggernaut, for example, is worth more than 40 Marauders, while the pardons price is only a factor 4. So, pardoning 80 Marauders to get 5% of 80 / 40 = 2 Juggernauts (so, 5% * 2 = 10% of one Juggernaut in total) could give you 5% on 80 / 4 = 20 Juggernauts (5% * 20 = one whole Juggernaut extra) if you pardon a Juggernaut instead of the Marauders.