I would say it depends on the reason the application is showing ads in the first place.
If it's an ad-supported app that has an option to pay to get rid of the ads, then definitely not — just pay the fee.
If it's a for-pay app where you already paid, with no mention of popup ads before you paid, and the company is now changing the deal and spamming you (cough Parallels Desktop) I'd say those ads are completely fair game for removal and discussion of methods should be allowed.
Apps that are ad-supported and don't offer an option to pay to go ad-free are more of a grey area — the author is surely allowed to make that choice, but on the other hand, it's reasonable to want to nuke in-app ads, particularly if they're insanely annoying.
Perhaps the best option here would be to find an alternative and see if the fall-off in users convinces the author to offer an ad-free option — but I would favour being allowed to discuss removal methods in this case, too.