I have always encouraged my students to play their guitar scales in an even manner. However, in the syllabus, the scales are written with a distinct rhythm (one, two and three and four and....etc) Which is the correct way to play these scales? Surely, so long as the scale is played evenly and consistently, then that's all that matters?Or am I wrong? I look forward to hearing other views.

For exam purposes, play the scales as they are written, with rhythms for the fingers only scales, straight crotchets for the thumb only, etc. They wouldn't have written them out that way if they didn't want them that way.
Of course, for general musical purposes a wider range of approaches can be helpful, including not just straight rhythms but dotted, swung etc.
If you look at the middle grades where the scales are over 2 octaves and in that rhythm, you may find it helps the player locate the tonic notes as they go through the scale, because its picked out as a crotchet. This can help build note knowledge in the middle of the fingerboard.

I also get pupils playing their scales ponticello and tasto (locating the octave point for the sweetest sound). Plus forte, piano MP MF ect..... As musically possible, I find this reflects in their pieces and adds more shape to Scalic style pieces!

Yes those are very good ideas. I think the point partly is that even though sometimes one aims for the most even, smooth, consistent sound possible, sometimes its precisely by introducing deliberate, controlled deviations from that quality, that evenness etc can be improved.