有一點　can only be used for bad things, but how about 一點？
Generally, people try to soften a negative assessment, or if you’re shy, downplay the intensity of your response. 
“The dish was too salty!” vs “The dish was a bit salty.”
“It’s too noisy, let’s get out of here!” vs “It’s a bit noisy in here, shall we go elsewhere?”
As you can see, no matter the language spoken, it’s not what you say but how you say it that matters. 

“有一點” serves this purpose in colloquial Chinese. I can’t imagine this phrase would be used in a professional or formal Chinese setting. It’s meant to downplay the intensity of your response. 

To answer your question, it’s not necessarily the case that this phrase is used to denote a negative connotation. 

“還不錯” 、”還可以” are other phrases used to downplay intensity of response. These are used to denote “is ok”. 
Example: 這本書還不錯，那本書很有意思！

I understand you were looking to highlight usage of “有一點”, but for your other example regarding desserts, I would favour something closer to:
這道點心不是很甜。
The tone is more assertive, appropriate for when you don’t care about offending the chef/dessert purchaser.