You are not overusing "that" as you are using it to stress a clause. In your sentence, using "that" helps you to emphasise on "I have done the forecast" and "the allowances paid to the employees...."
Notice the lack of emphasis if you were to write: "Please note I have done the forecast assuming the allowances paid to the employees (e.g. travelling etc.) will remain same in the coming 10 years."
(A) It all happened so fast I had no time to react.
(B) It all happened so fast that I had no time to react.
("that" is used to emphasise your lack of reaction time.)
On a separate note, I would edit your sentence slightly:
Please note that I have done the forecast assuming that the allowances paid to the employees (1) (e.g. travelling) will remain (2) [the] same in the (3) [next ten] years.
(1) When you provide examples, it is understood that you are not providing the entire list. Therefore, you do not need to use "etc.". (e.g. accounts payable, accounts receivable, balance sheet)<-- correct
(e.g. accounts payable, accounts receivable, balance sheet etc.)<-- incorrect
(2) As you are referring to a specific amount of money (allowance) that an employee can claim, you use the definite article "the".
(3) We use "coming" merely to refer to something imminent or happening soon. I believe you are actually referring to ten years that immediately follow the current year. To express this meaning, we use "next".
Next, this is a general rule: If the number is of a small value, we describe it in words (i.e. ten instead of 10).
Look at this example: There are four possible answers for these ten multiple-choice questions. (correct) / There are 4 possible answers for these 10 multiple-choice questions. (the sentence can still be understood, but it distracts the reader with a mixture of words and numbers.)
Of course, there are exceptions where numbers must be used. Examples include units of measure (e.g. 10%, 5 kg, $7.80)
I hope this helps you.