How can I do a conditional SQL?

a) You would be better using ANSI syntax SQL so you can clearly differentiate between your join conditions and filter (WHERE Clause) conditions...

b) Clearly your schema has been designed by people who have no idea about good table or column naming. So, aliasing your tables with exactly the same nonsensical name doesn't help others to understand and debug code, now or in the future. Choose aliases that actually mean something, or at the very least don't alias with exactly the same as the table name.

c) Ensure you specify which table/alias the columns are coming from, so others don't have to guess.

d) Avoid double quoting column aliases, as it makes the result case sensitive and causes a massive headache for anyone having to use it in code as they would also need to know the exact case used throughout. It's generally considered bad practice.

select 
  FQ7076E3.FEQ70NN as Numero_Comprobante, -- avoid double quoting column names which makes them case sensitive
  FQ7076E3.FEQ70NAU2 as Numero_Autorizacion,
  F0101.ABTAX as RUC_Emisor,
  to_date(to_date(1900000 + FQ7076E3.FEIVD, 'yyyyddd'),'DD/MM/YYYY') as Fecha_Emision,
  to_date(to_date(1900000 + FQ7076E3.FEUPMJ, 'yyyyddd'),'DD/MM/YYYY') as Fecha_Autorizacion,
  FQ7076E3.FETAX as ID_Fiscal,
  FQ7076E3.FEALPH as Razon_Social,
  <table>.DOCUMENT_TYPE_1, -- specify the table/alias for the field, I assume this is "DOCU."
  sys.dbms_lob.getlength("DOCUMENT_TYPE_1") as Archivo_PDF,
  DOCU.DOCUMENT_FILENAME_1,
  DOCU.DOCUMENT_MIMETYPE_1,
  <table>.DOCUMENT_TYPE_2, -- specify the table/alias for the field, I assume this is "DOCU."
  sys.dbms_lob.getlength("DOCUMENT_TYPE_2") as Archivo_XML,
  DOCU.DOCUMENT_FILENAME_2,
  DOCU.DOCUMENT_MIMETYPE_2
from F0101
     join F0010 on F0010.CCAN8=F0101.ABAN8
     join FQ7076E3 on FQ7076E3.FECO=F0010.CCCO
     left outer join F_ASR_DOCUMENTS DOCU on DOCU.DOCUMENT_ID = FQ7076E3.FEQ70NN
where <table>.FEDL02 = '03' -- specify the table/alias for the field
and   <table>.FEQ70DTP = '2' -- specify the table/alias for the field
and (    :is_admin = 1 -- If user is admin it shows all records
     or (    :is_admin = 0 -- If not admin show records for the app_user
         and trim(FQ7076E3.FETAX) = coalesce(:APP_USER, USER)  -- Trim(coalesce(sys_context('APEX$SESSION','APP_USER'),user))
        )
    )

Your use of sys_context from apex$session is lengthy, and Apex provides the shorter version of :APP_USER, so simplify your code to make it more readable. (also no need to trim the user names, they shouldn't have space around them).

The only reason I can think of that that logically wouldn't work and not give you the results in the way you describe would be if there was a NULL value being tested, i.e. :is_admin is null, in which case it's neither 1 nor 0.

Ensure your variable has been correctly populated.