You need to decide what it is you are trying to do first.
If you want to have a struct with a pointer to an [independent] array inside, you have to declare it as
struct my_struct {
int n;
char *s;
};
In this case you can create the actual struct object in any way you please (like an automatic variable, for example)
struct my_struct ms;
and then allocate the memory for the array independently
ms.s = malloc(50 * sizeof *ms.s);
In fact, there's no general need to allocate the array memory dynamically
struct my_struct ms;
char s[50];
ms.s = s;
It all depends on what kind of lifetime you need from these objects. If your struct is automatic, then in most cases the array would also be automatic. If the struct object owns the array memory, there's simply no point in doing otherwise. If the struct itself is dynamic, then the array should also normally be dynamic.
Note that in this case you have two independent memory blocks: the struct and the array.
A completely different approach would be to use the "struct hack" idiom. In this case the array becomes an integral part of the struct. Both reside in a single block of memory. In C99 the struct would be declared as
struct my_struct {
int n;
char s[];
};
and to create an object you'd have to allocate the whole thing dynamically
struct my_struct *ms = malloc(sizeof *ms + 50 * sizeof *ms->s);
The size of memory block in this case is calculated to accommodate the struct members and the trailing array of run-time size.
Note that in this case you have no option to create such struct objects as static or automatic objects. Structs with flexible array members at the end can only be allocated dynamically in C.
Your assumption about pointer aritmetics being faster then arrays is absolutely incorrect. Arrays work through pointer arithmetics by definition, so they are basically the same. Moreover, a genuine array (not decayed to a pointer) is generally a bit faster than a pointer object. Pointer value has to be read from memory, while the array's location in memory is "known" (or "calculated") from the array object itself.