Fortunately, a good research worker have an intuition which may prompt them to think about the practical applications of their work. A basic awareness of these possibilities has to be in the mind of the research worker in the first place. The answer is yes to both parts of the question. Having the help of someone skilled in patent law will not guarantee the absence of problems for the simple reason that there will always be official objections which are difficult to overcome. A distinction is also to be made between invention and innovation.
Invention requires a stricter standard of novelty.
Top Secrecy seems to be an alternative option to patenting. Patenting an invention or keeping it secret are incompatible options. Patents were invented to induce disclosure of new technology and therefore enable society to benefit from the knowledge of it as well. For most research workers, this option of secrecy is unattractive because it would be difficult to keep a vow of perpetual silence. The conclusion is that if you are under pressure to publish in the journals, you will need to consider seriously the possibility to patent protection in your case.