For example, i have around 1000 notes in markdown, is it ok to import them all using the import feature?
Should be fine. If you have reservations, you could create an extra throw-away profile and test the import there, and if all is well then import your markdown notes into your main profile?
The most important thing is that any links (links to other notes, image resources, etc...) are in markdown format, not wikilinks format.
UPDATE: completed the import. Everything went well. Some notes are kinda “broken” because used another markdown flavor, but it all can be rewritten.
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If you have to make some global replacements you might find this plugin useful: Joplin Batch.
To find notes with special characters that Joplin Batch can't handle, Edit > Search in All Notes is useful, to at least gather those target notes into the note list. E.g., if I wanted to find the fence notation :{:{ I would search by entering this syntax in the search box /":{:{"
Good luck with tidy up!