php how to store and read json data via mysql?

Technically, you are going the wrong way with that. MySQL is used to store each of your ID/VALUE seperately. For the sake of NOT changing your code we'll look at your solution first but then i'll explain the "better" way of doing it.

First, you need to make your JSON as a variable, not part of your SQL:

mysql_query("INSERT INTO text (data) VALUES (".mysql_real_escape_string(array(json_encode('id' => $uid, 'value' => 'yes'))).")");

instead of

mysql_query("INSERT INTO text (data) VALUES (json_encode('id' => $uid, 'value' => yes))");

This first part will allow you to at least instead the data correctly into mysql. I am ASSUMING your table has an ID and that you will be using it to update or delete

When you retrieve your data, you can json_decode the $row['data'] to get your data back from the row and work with it. To update it, just do:

mysql_query("UPDATE text SET data = "'.mysql_real_escape_string(json_encode($myJsonToBeData)).'" WHERE rowid = '.$myrowid)

Now, for the RIGHT way to do this:

The right way to do this would be to have these fields into your table: ID, JSONID, JSONVALUE and use this SQL instead:

SELECT * FROM text WHERE id = $rowid
INSERT INTO text VALUES(NULL, $jsonid, $jsonvalue)
UPDATE text SET jsonid = $jsonid, jsondata = $jsondata

This is pretty basic, but it will allow you to have any number of entries in your database that make it searchable, indexed, sortable, queryable, etc...

Yes but....WordPress stores a lot of its data as encoded JSON strings, such as the user capabilities. Storing an array as a discrete bit of data takes away having to do multiple reads on the database and allows you to get a lot of data on one read. If you never see the need to SELECT the individual parts of the JSON string I don't see why it isn't acceptable to do it this way. MySQL must think so too because it has functions to allow a SELECT on the individual fields within a JSON string if you so desired (see MySQL EXPLAIN keyword). But I do agree if you were going to do a lot of SELECTs on a field it should have one of its own. It all depends on how you are going to use the data.

You can do this more efficiently by NOT storing JSON in a single field but by creating a proper MySQL table with the JSON object's property names as field names.

Storing a text-string encoded representation of your data in a database completely destroys the point of using databases in the first place.