The OS is protected without doubt and they have previously threatened actions of the mock ups
-aqua wiki
Most cases are old or not mentioned
http://www.macworld.com/article/1021072/stardock.html
And it says it well, its a murky area. Everyone gets inspiration from something, and you cant claim ownership to someone elses work because yours inspired it if it is quite different. The line for copyright on a GUI is if it is "easily confused with another by an average user". So they can protect aqua all day, but the feel of it will be the factor that decides the legality. The feel can be remarkably close as long as its easily distinguished.
But the use of water like effects. lots of shadows and reflections, and layout won't be enough. When apple went against MS about an aqua skin it was focused on the way the skin was described(Pearl dug their grave with that) and the icons. Images, Icons, and other small features may spare them.
That being said, if you ever saw Pear OS(mac OS like Linux) it was rumored apple cause it to go bye-bye, but no end users were taken out. I would imagine that if Pearl is found to be "confusingly similar" to OSX then the same will happen.
I would also refer you to the constant battle of Apple and Samsung.
So as of now it is legal, will it be in a year is another question.
Will it ever effect you? only if and when apple forces Pearl to end support.
On another note, I would recommend you use another linux is its for daily use, not only because Pearl has a small community but they also note their own instability. Linux is able to be customized to about anything(Ricing) and ubuntu has many GUI options(gnome and kde, the ones used in Pearl). and a large community to help with such.