I have to agree with this as far as my personal experience goes. Whenever I tried thinking "licks", it always seemed detrimental for my practicing/learning, but it seems to be helpful for others.I believe that's essential to being equally fluid in all keys. I, however, don't refer to technical exercises as "licks", though. Do you? When I hear someone speak of practicing licks, I think of improvisational patterns, such as for ii-V-I progressions and the like, and that's typically what is meant. This is not necessary and, in some cases, is even detrimental to creativity. The key to complete freedom and flexibility in improvisation is three-fold: 1) Listen to and transcribe as much as you possibly can and, if you can, compose (to expand your ears and develop ideas); 2) Play changes by ear as much as possible and, when practicing, sing pitches, arpeggios, and the like aloud and then try to be as precise as you can in finding them on your instrument (to really connect your ear to your instrument, such that you can find anything you hear in your mind's ear on your instrument); and 3) Develop your technique as much as you can (to allow your fingers to be able to keep up with what you're hearing).
Without pushing anyone into agreeing with this (but I'm sure many do), I would really advice the topic's starter to try seeing it in a "systemic" manner: Because, learning to relate different notes in different contexts (for example, keys, chord changes, styles of music, etc.), and being fluent at this, helps improvising in a free, intuitive, may I say playful way, and most importantly: not get 'stuck' repeting licks "where it fits".
Of course, practice many times should differ from "actual playing", BUT excercising your ears in this systemic (or organic) way of playing with relationships between notes WILL transfer to your improvised playing and I specially agree with renassaince_man here: it WILL show!
In a systemic approach to playing you take each note not separate but as a part of an intricate web of relations. So, you learn to understand that the note C can adopt so many different shapes wether the context it's being played on changes. It's never the same C. And you must get comfortable with the different relations the note C has and how they sound. It's not that you just comprehend that the 4th note is a half step from the 3th note in the lick, you need to comprehend what the relationships between the notes in this structure "means"=sounds like. If the lick you like to understand seems hard, break it down into subsystems to comprehend the relationships.
Now, rather than practicing 'licks', try practicing different intervals in different keys and contexts, try mixing them, try making varied structures of intervals (this is what a 'lick' tends to be, anyway) and varying the context, etc.
Keys are also structures of intervals, so you can play around with this idea a lot. The sound is always in the relationship between elements of the system.
Lastly, I don't believe thinking while playing is entirely wrong, sometimes thinking about trying something different than what first comes to your fingers actually has some very good results, and it can be the step towards innovation in that particular time. To example this: I was once improvising on a "modal" reggae tune, my ear was feeling a little too "conventional" as far as my ideas, so for a second I thought about varying certain elements to give me a new direction (just as a fist step) and it brought me fun results
In this example, thinking was used to get out of "what works" instead of looking for it to be safe. I believe in learning to not be safe!
--I'm sorry for the long post! Good luck!