My friend won 'best in breed' with her 7mth pup (no CCs available), she's just about to enter Manchester but can she still enter him in 'puppy'?

Of course, even if he had won CC's the class is defined by age not wins.

Thank you :) does that change in other classes? Im sure I had to enter open once I had my first CC in Limit?

If it was a Champ Show, with more than three classes, five classes for Stud Book band E she will have qualified for Crufts.
BOB and Best Puppy now qualifies. See Crufts Schedule Page 4 Section b Additional Entry Into Breed Classes.

In an age defined class that is Minor Puppy, Puppy, Junior, Yearling or even Veteran it does not matter how many CCs have been won if your dog is of the correct age then they can enter the class.

Anything won at a championship show where there are no CCs on offer for that breed then it is treated as if it is a Open Show.

None of this makes any difference to qualification to Crufts as this has nothing to do with which class you are over qualified for and is a totally different matter.

Thanks Nova :)

Im sure I had to enter open once I had my first CC in Limit?

You can enter Limit with 2 CCs -it is various class wins that counts (not more than 7 wins in Limit and Open at shows with tickets available), and not having a Champion title either here or abroad.