The tense used disambiguate the sentence:

Asking if they are always here, not only during the period of time we are talking about:

Sont-ils là tout le temps ?

Asking if they have been here the whole time we are talking about:

Ont-ils été là tout le temps ?

Asking if they will be there the whole time we are talking about:

Seront-ils là tout le temps ?

1.”Toujours” is not very precise;

–Depuis que je suis arrivé à l’hôtel il y a six semaines, il y a certains clients que je n’ai pas cessé d’y voir. Sont-ils là tout le temps ?

The addition of “y” (which stands for “hotel”) makes the sentence more explicit.

2.Let’s take up the following sentence;

Translation: Since arriving 6 weeks ago, there have been certain clients that I’ve always seen. Have they been here the whole time.?’

Something is not right: “the whole time” has to refer to a specific time and that time can only be the time from the arriving to the end of the six weeks; how can the person ask about those clients being there during that time (that whole time) when it is the same person saying that he/she has seen those clients there? Is it possible that you mean something else? For example do you mean that although you saw the clients now and again during the six weeks you do not know whether their stay at the hotel was a continuous one? That seems the only other possible case; if that is so then you might want to phrase your question as follows;

–Depuis que je suis arrivé à l’hôtel il y a six semaines, il y a certains clients que je n’ai pas cessé d’y voir. Sont-ils restés dans cet hôtel six semaines d’affilée ?

3. Your first sentence indicates the opposite of what you want to say; it says that you want to know whether from an indeterminate date before you arrived those clients were at the hotel and kept on being there thereafter.

In order to make the distinction you want it is necessary to make the context more precise, as in number 2 above.

Your first remark is quite right: “tout le temps” can mean “the whole time” or “all the time”. For example:

Ne t'inquiète pas, nous avons tout le temps

means:

Don't worry, we have the whole time

Though I think that here, English people might as well use “all the time”, but not in the sense of “always”.

And now the other sense:

Tu te trompes tout le temps

This time, we can translate it: “You always make that mistake”. So here, “tout le temps” doesn’t mean “the whole time” but “always” or “every time”.

And now, your example. First, you made two little mistakes: you should have typed

“certains clients que j’ai toujours vus“

instead of

“certaines clients que j’ai toujours vu“.

Secondly, the phrase “sont-ils là tout le temps” doesn’t mean “the whole time”, but “always”: If you wanted to express “the whole time”, you should have used “tout ce temps” instead of “tout le temps“:

Ont-ils été là tout ce temps?