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An LED may tear down a signal on its input to a non-conformant value, so this might disturb programming. On the other hand I2C, SPI and other usages of the ISSP header-pins do not disturb the programming.
My experiences with Cypress are: you can trust the TRMs and datasheets. Only problems are that sometimes something is not listed and you have to ask Cypress for. When the (latest) manual states that a 1K resistor to LED will work then you may use it as indicated.