Personally, I think you are probably correct in the fact that you could be seen to be damaging your social reputation as so many tweets could be considered spammy.
The problem is you will be constantly flooding your followers twitter accounts with simply too many automated tweets, I would seriously recommend slowing it down and tweeting only a few key times a day with relevant content that people will want to retweet, favourite or comment on,
Also and this is only from my stand point, try and interact with people rather than being a blank faced corporate tweeting entity, this will most likely help you to become real and in that case hopefully attract more followers.
EDIT : As such it is not necessarily Hootsuite that is the issue.... Maybe just schedule in the odd tweet a couple of times a day.