So you want to deprecate something in OTB? Follow the guide:

A C++ class

In the doxygen documentation of the class, add the \deprecated keyword.

A method of a C++ class or free function

In the doxygen documentation of the method, add the \deprecated keyword.

A part of the Python API

An OTB application

Add the deprecated tag to DoInit() section:

AddDocTag(Tags::Deprecated);

An OTB module

An OTB module can be deprecated thanks to the otb_module macro in the otb-module.cmake. One just need to add the key word DEPRECATED the arguments.
Here is an example of th otb-module.cmake of a deprecated module :

set(DOCUMENTATION "Some documentation")
otb_module(OTBDeprecatedModuleName
  DEPENDS
    OTBSomeDependencies

  TEST_DEPENDS
    OTBTestKernel
    OTBSomeOtherDependenciesForTest
  
  DEPRECATED

  DESCRIPTION
    "${DOCUMENTATION}"
)

One need to make sure that the deprecated module is not a mandatory dependency of any other module. One can still allow the module to be used thanks to the OPTIONAL_DEPENDS key word :

set(DOCUMENTATION "Some documentation")
otb_module(OTBDModuleName
  DEPENDS
    OTBSomeDependencies
  
  OPTIONAL_DEPENDS
    OTBSomeOptionalDependencies
    OTBSomeDeprecatedModule

  TEST_DEPENDS
    OTBTestKernel
    OTBSomeOtherDependenciesForTest

  DESCRIPTION
    "${DOCUMENTATION}"
)

Please make sure that all of the classes, methods and free functions in the module have the ModuleName_DEPRECATED_EXPORT and the Doxygene tag \deprecated.