Actually, it's likely that the database is storing the numbers as numbers, but that the format used when a number is retrieved from the database specifies commas. For example, in Oracle SQL*PLUS:

14:23:48 FOCX> desc mytable
 Name                                      Null?    Type
 ----------------------------------------- -------- ----------------
 ID                                                 NUMBER(7)       

14:23:56 DB> select id from mytable;
Press <enter> to continue...
     ID
-------
   1000
   1001
 
14:23:59 DB> set numformat 999,990
14:24:06 DB> /
Press <enter> to continue...
      ID
--------
   1,000
   1,001
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