It's certainly a possibility. You could try changing the construct to put the His-tag at the C-terminus. You could also use a cleavable tag construct so that the His-tag can be removed after purification. It's also possible that the recombinant protein is not correctly folded.

Try C-terminal His-tag or introduce a protease cleavage site between the His-tag and N-terminus of your recombinant protein.

You could use another affinity matrix domain, like maltose, instead of His-tagging.

The His-tagged residues may be chelating the metal ion cofactors required for endolysin activity.

Nterminus histag has the problem of possible truncation. If the protein is truncated then it will still bind to the ni column.

The short answer is yes, you may be masking an important part of your protein. Moving the tag to the other end may restore the functionality.