Remove deprecated methods from NWBFile #1637

Job	Run time
conda-linux-gallery-python3.13-ros3	1m 28s
linux-gallery-python3.9-minimum	2m 7s
linux-gallery-python3.13-upgraded	4m 25s
windows-gallery-python3.9-minimum	2m 52s
windows-gallery-python3.13-upgraded	8m 16s
conda-linux-python3.13-ros3	1m 29s
linux-python3.9-minimum	7m 24s
conda-linux-python3.9-minimum	6m 37s
linux-python3.13-upgraded	6m 7s
conda-linux-python3.13-upgraded	5m 32s
windows-python3.9-minimum	8m 5s
windows-python3.13-upgraded	7m 51s
macos-python3.9-minimum	9m 15s
macos-python3.13-upgraded	3m 50s
Deploy pre-release from dev	0s
	1h 15m 18s

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