Playing same notes in different positions

Yes, there's a difference. But it might not be important.

Sounds are made up of several different factors, and what you're talking about covers two of them - pitch and timbre. Pitch is how high or low a note is... timbre is the "quality" of the sound.

No matter where you fret a note, the pitch is the same; the open 1st string is the same pitch as the 2nd string 5th fret, 3rd string 9th fret, 4th string 14th fret, etc. But they don't sound exactly the same.

Each position has subtle differences in the overtones produced, and that's affected by the length of the string from the fret to the bridge, whether the string is wound or plain, the gauge of the string, etc. Some differences are going to be bigger than others.

So if you hear a difference, it's big enough to be important - make a musical decision. If you don't hear a difference, or if there isn't enough of one to worry about, make a technique-based decision.

Some technique-based decisions might include:
Efficiency:
Choosing to play notes in a location that is close to the previous notes and/or following notes. You don't want to be jumping all over the fretboard if you can help it. Less movement = more efficiency.
Vibrato:
Whether you can achieve vibrato at the lower frets as effectively as you can at the higher frets. That applies to bending too.
Intonation:
If you're unfortunate enough to be playing a cheap and nasty or badly set up guitar, it might sound fine at the nut and lower frets but become increasingly out of tune the higher up the fretboard you go.

Open strings present different choices again. They are a two-edged sword. On the plus side, open strings are great as you can play them even if all your other fingers are busy with other notes. Open strings can sustain freely, providing the required harmony while your fingers move off to do other things on other strings.
On the downside, that freely sustaining open string doesn't know when to stop and can just as easily provide the WRONG harmony as it clashes with the notes on other strings immediately following it, unless you take steps to mute it. Not a problem with fretted strings that are completely under your control. Also there's no vibrato with open strings. If you play a slow melodic phrase with a warm vibrato, any note on an open string will sound noticeably and disappointingly 'colder' as the vibrato suddenly stops. Last one I can think of - pulloffs. You can't pull off from an open string.

I was going to reply, but I think you two ^^^ have covered it pretty thoroughly. I never really thought about all of the technique-based decisions, I usually just make sure it's efficient to play it the way I am. So thanks a lot Fretsource for all the info.

thanks to you both for comprehensive information

at the moment i agree with the ideas about open notes being a bit more difficult, and i can visualise the pattern easier at the higher frets, as the riffs i'm talking about both occur in the pentatonic box patterns, whereas down the fretboard i find it a bit harder to visualise

thanks again