Using Hootsuite is no different than using a tool like Tweetdeck, Seesmic or Brizzly.

Hootsuite doesn't do any sort of automated posting. It is simply a tool you can use to make your day to day social media management a little easier. It does allow you to cross post to multiple accounts but there is nothing automated about this process.

Tools such as Hootsuite offer additional features not found within the social networks own websites such as analytics and automatic URL shortening and yes it is best to craft your message specifically for each social network (which you can do from within Hootsuite) you are posting to as each has different requirements but if you can save a lot of time by using one tool why wouldn't you want to do that?

I don't think hiding or blocking messages and content sent from specific applications is the proper solution that's like deleting Outlook because your email inbox receives spam. If you are experiencing spam or spam related issues that is a user issue and not an application issue and in my opinion it would be best to block, unfollow or unfriend that individual and not block the application. You may find that you are missing out on some very valuable and interesting content going through your Facebook and Twitter streams because of the applications you block.